Integration of sample storage and sample management for life science

ABSTRACT

Compositions and methods are disclosed for automated storing, tracking, retrieving and analyzing biological samples, including dry storage at ambient temperatures of nucleic acids, proteins (including enzymes), and cells using a dry storage matrix that permits recovery of biologically active materials. RFID-tagged biological sample storage devices featuring dissolvable or dissociable matrices are described for use as supports of biological samples, which matrices can be dried and subsequently rehydrated for sample recovery. Also disclosed are computer-implemented systems and methods for managing sample data.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a divisional application of U.S. patent applicationSer. No. 11/102,588 now U.S. Pat. No. 8,900,856, filed Apr. 8, 2005,which application claims the benefit of U.S. Provisional PatentApplication No. 60/560,829, filed Apr. 8, 2004, which applications areincorporated herein by reference in their entirety.

TECHNICAL FIELD

The present invention relates generally to processes by which biologicalmaterials and samples are received and placed into inventory systems.The invention also relates to the use, organization, storage, tracking,retrieval and analysis of such biological materials and samples and tothe automation of these processes.

BACKGROUND OF THE INVENTION

Research in the life sciences field is based upon the analysis ofbiological materials and samples, such as DNA, RNA, blood, urine, buccalswabs, bacteria, viruses, PCR products, cloned DNA, proteins, cells andtissues, and of minerals or chemicals. Such samples are typicallycollected or obtained from appropriate sources and placed into storageand inventory for further processing and analysis.

Storage containers for such samples include bottles, tubes, vials, bags,boxes, racks, multi-well dishes and multi-well plates which aretypically sealed by individual screw caps or snap caps, snap or sealclosures, lids, adhesive strips or tape, or multi-cap strips. Thestandard container format for medium to high throughput of samplestorage, processing and automation of biological processes is a 96-,384-, or 1536-well plate or array. The containers and the samplescontained therein are stored at various temperatures, for example atambient temperature or at 4° C. or at temperatures below 0° C.,typically at about −20° C. or at −70° C. to −80° C. The samples that areplaced and stored in the devices are most frequently contained in liquidmedium or a buffer solution, and they require storage at such subzerotemperatures (e.g., −20° C. or −70 to −80° C.). In some cases, samplesare first dried and then stored at ambient temperature, or at 4° C., at−20° C. or at −70 to −80° C.

For example, presently, nucleic acids are stored in liquid form at lowtemperatures. For short term storage, nucleic acids can be stored at 4°C. For longterm storage the temperature is generally lowered to −20° C.to −70° C. to prevent degradation of the genetic material, particularlyin the case of genomic DNA and RNA. Nucleic acids are also stored atroom temperature on solid matrices such as cellulose membranes. Bothstorage systems are associated with disadvantages. Storage under lowtemperature requires costly equipment such as cold rooms, freezers,electric generator back-up systems; such equipment can be unreliable incases of unexpected power outage or may be difficult to use in areaswithout a ready source of electricity or having unreliable electricsystems. The storage of nucleic acids on cellulose fibers also resultsin a substantial loss of material during the rehydration process, sincethe nucleic acid stays trapped by, and hence associated with, thecellulose fibers instead of being quantitatively recoverable. Nucleicacid dry storage on cellulose also requires the separation of thecellulose from the biological material, since the cellulose fibersotherwise contaminate the biological samples. The separation of thenucleic acids from cellulose filters requires additional handling,including steps of pipetting, transferring of the samples into new tubesor containers, and centrifugation, all of which can result in reducedrecovery yields and increased opportunity for the introduction ofunwanted contaminants or exposure to conditions that promote sampledegradation, and which are also cost- and labor-intensive.

Proteins are presently handled primarily in liquid stages, in cooled orfrozen environments typically ranging from −20° C. to storage in liquidnitrogen. In some exceptions proteins may be freeze-dried, or dried atroom temperature in the presence of trehalose and applied directly to anuntreated surface. (Garcia de Castro et al., 2000 Appl. Environ.Microbiol. 66:4142; Manzanera et al., 2002 Appl. Environ. Microbiol.68:4328) Proteins often degrade and/or lose activity even when storedcooled (4° C.), frozen (−20° C. or −80° C.). The freeze-thaw stress onproteins reduces bioactivity (e.g., enzymatic activity, specific bindingto a cognate ligand, etc.) especially if repeated freeze-thawing ofaliquots of a protein sample is required. The consequent loss of proteinactivity that may be needed for biological assays typically requires thereadjustment of the protein concentration in order to obtain comparableassay results, or costly rejection of compromised protein reagents infavor of procuring new lots. The common practice of having multiple usesof enzyme reagents stored in a laboratory, especially by different usersat different times and employing non-standardized handling procedures,further reduces the reliability of experimental data generated with suchreagents. As a result, the half-life of proteins is reduced andexpensive reagents have to be replaced frequently, amounting to enormousfinancial costs to the user. For the supplier of the proteins high costsare required to maintain an undisrupted frozen supply chain startingwith initial cold room work-ups, for shipment, frozen storage of thesample, and frozen transport of the protein from production to the siteof use. For example, delays during shipment can result in inactivationof proteins, which then have to be replaced at great cost to thesupplier; receipt of inactive product can also result in dissatisfiedcustomers.

Drying of proteins, and nucleic acids has yet to be universally adoptedby the research scientific, biomedical, biotechnology and otherindustrial business communities because of the lack of standardestablished and reliable processes, difficulties with recoveries ofquantitative and functional properties, variable buffer and solventcompatibilities and tolerances, and other difficulties arising from thedemands of handling nucleic acids and proteins. The same problems applyto the handling, storage, and use of other biological materials, such asviruses, phage, bacteria, cells and multicellular organisms.

Present sample storage containers represent a multitude of platformswith no unified approach to sample preparation, sample storage, sampleinventory, sample tracking, sample retrieval and sample analysis. It isclear that none of the current sample processing and storage formatssolve problems that arise from individual storage containers, inadequateclosure and containment aids, sample contamination, inadequateorganization, diverse labeling systems, large space and storagerequirements and temperature constraints.

The genomic age and the recent deciphering of the human and many othergenomes, proteomes, transcriptomes, etc. have led to theindustrialization of life sciences research. Millions of biologicalsamples including genes and/or gene products from a multitude oforganisms are being analyzed in order to advance scientific knowledgeand develop commercial products. The development of high throughputtechnologies has resulted in a vast pool of information and samples,such that there is a need to integrate sample storage, data organizationand data analysis. The generation of myriad biological samples and dataconsequently poses a significant organizational challenge to small andlarge laboratories. Previously available data management options forlife sciences samples, such as LIMS (Laboratory Information ManagementSystems), are incapable of integrating information pertaining to aparticular sample or samples with a sample storage device, and typicallystore sample data on a central server that is neither physically norelectronically connected to the sample storage device. Moreover, suchpreviously available systems require inconvenient storage rackconfigurations, typically involving cumbersome cold storage and/orcostly, complex software that requires a dedicated full-time InformationTechnologies support professional regardless of whether a large-scaleenterprise software system is to be purchased and configured to aparticular user's needs, or if instead a customized program is to beindependently developed.

Clearly there is a need in the industry for universal life sciencessample storage, retrieval, analysis and information-matching devices andsystems. The present disclosure addresses such needs by providing aplurality of life sciences sample storage and data applications, andoffers other related advantages.

SUMMARY OF THE INVENTION

It is an aspect of the present invention to provide a system forprocessing data regarding the storage, organization, tracking,retrieval, and analysis of biological samples, the system including abiological sample device; a computer-implemented system for receiving,storing, processing, and communicating data regarding the sample device;and a radio frequency interface between the sample device and thecomputer-implemented system for providing a communication link betweenthe computer-implemented system and the sample device.

According to the several embodiments of the invention, there areprovided the following: A biological sample storage device for one or aplurality of biological samples, comprising: (a) a lid; (b) a sampleplate comprising one or a plurality of sample wells that are capable ofcontaining a biological sample, wherein one or more of said wellscomprises a matrix material; and (c) at least one radio frequencytransponder device. A related biological sample storage device whereinthe matrix material dissolves or dissociates in a solvent or whichcomprises a closure means for closing the lid onto the sample plate,optionally wherein further the closure means comprises a magneticclosure. A related biological sample storage device which comprises anairtight closure joint, or comprising an airtight closure joint aroundeach well, or comprising a magnetic closure and an airtight closurejoint around each well. In certain embodiments there is provided arelated biological sample storage device wherein the matrix material iscapable of dry storage of the sample without refrigeration.

In other embodiments the invention provides a biological sample storagedevice for one or a plurality of biological samples, comprising (a) alid; (b) a sample plate comprising one or a plurality of sample wellsthat are capable of containing a biological sample, wherein one or moreof said wells comprises a matrix material that dissolves or dissociatesin a solvent; and (c) at least one radio frequency transponder device.In certain further embodiments of the above described biological samplestorage device, at least one well comprises at least one detectableindicator, which in certain further embodiments comprises a colorimetricindicator, and which in certain other embodiments is a fluorescentindicator, a luminescent indicator, a phosphorescent indicator, aradiometric indicator, a dye, an enzyme, a substrate of an enzyme, anenergy transfer molecule, or an affinity label. In certain other furtherembodiments the detectable indicator is capable of detectably indicatingpresence of at least one of an amine, an alcohol, an aldehyde, water, athiol, a sulfide, a nitrite, avidin, biotin, an immunoglobulin, anoligosaccharide, a nucleic acid, a polypeptide, an enzyme, acytoskeletal protein, a reactive oxygen species, a metal ion, pH, Na⁺,K⁺, Cl⁻, a cyanide, a phosphate and selenium. In certain other furtherembodiments the detectable indicator is selected from the groupconsisting of phenol red, ethidium bromide, a DNA polymerase, arestriction endonuclease, cobalt chloride, Reichardt's dye and afluorogenic protease substrate.

According to certain other related embodiments the biological samplestorage device comprises at least one well that comprises at least oneinhibitor that is a biological inhibitor or a biochemical inhibitor,which may be validamycin A, TL-3, sodium orthovanadate, sodium fluoride,N-α-tosyl-Phe-chloromethylketone, N-α-tosyl-Lys-chloromethylketone,aprotinin, phenylmethylsulfonyl fluoride, diisopropylfluoro-phosphate, akinase inhibitor, a phosphatase inhibitor, a caspase inhibitor, agranzyme inhibitor, a cell adhesion inhibitor, a cell divisioninhibitor, a cell cycle inhibitor, a lipid signaling inhibitor and aprotease inhibitor, a reducing agent, an alkylating agent, or anantimicrobial agent. In certain embodiments the matrix material iscapable of dry storage of the sample without refrigeration, in certainembodiments the matrix material comprises polyvinyl alcohol, and incertain other embodiments the matrix material comprises at least onematerial selected from polyethylene glycol, agarose,poly-N-vinylacetamide, polyvinylpyrrolidone, poly(4-vinylpyridine),polyphenylene oxide, crosslinked acrylamide, polymethacrylate, carbonnanotube, polylactide, lactide/glycolide copolymer, hydroxymethacrylatecopolymer, calcium pectinate, hydroxypropyl methylcellulose acetatesuccinate, heparin sulfate proteoglycan, hyaluronic acid, glucuronicacid, thrombospondin-1 N-terminal heparin-binding domain, fibronectin, apeptide/water-soluble polymeric modifier conjugate, collagen,hydroxyectoine, polystyrene or trehalose. In another embodiment theinvention provides a kit, comprising (I) a biological sample storagedevice for one or a plurality of biological samples, comprising (a) alid; (b) a sample plate comprising one or a plurality of sample wellsthat are capable of containing a biological sample, wherein one or moreof said wells comprises a matrix material; and (c) at least one radiofrequency transponder device; and (II) one or more ancillary reagents.In certain further embodiments the matrix material dissolves ordissociates in a solvent

Turning to another embodiment of the invention, there is provided amethod of storing one or a plurality of biological samples, comprisingcontacting one or a plurality of biological samples with a biologicalsample storage device, said biological sample storage device comprising(i) a lid, (ii) a sample plate comprising one or a plurality of samplewells that are capable of containing a biological sample, wherein one ormore of said wells comprises a matrix material, and (iii) at least oneradio frequency transponder device, and thereby storing said biologicalsamples, the method in certain further embodiments comprisingmaintaining the biological sample storage device without refrigerationsubsequent to the step of contacting. Another invention embodimentprovides a method of storing one or a plurality of biological samples,comprising (a) contacting one or a plurality of biological samples witha biological sample storage device, said biological sample storagedevice comprising (i) a lid, (ii) a sample plate comprising one or aplurality of sample wells that are capable of containing a biologicalsample, wherein one or more of said wells comprises a matrix materialthat dissolves or dissociates in a solvent, and (iii) at least one radiofrequency transponder device; and (b) drying one or more of the samplewells, and thereby storing said biological samples, the method incertain further embodiments comprising maintaining the biological samplestorage device without refrigeration subsequent to the steps ofcontacting and drying, wherein in certain still further embodimentsbiological activity of the sample subsequent to the step of maintainingis substantially the same as biological activity of the sample prior tothe step of contacting, and wherein in certain other still furtherembodiments degradation of the biological sample is decreased relativeto degradation of a control biological sample maintained withoutrefrigeration in the absence of the matrix material. In certain relatedembodiments the step of contacting comprises simultaneously dissolvingor dissociating the matrix material in a solvent, while in certain otherrelated embodiments the step of contacting is preceded by dissolving ordissociating the matrix material in a solvent, while in certain otherrelated embodiments the step of contacting is followed by dissolving ordissociating the matrix material in a solvent.

In another embodiment the invention provides a method of preparing abiological sample storage device for one or a plurality of biologicalsamples, comprising (a) administering a matrix material that dissolvesor dissociates in a solvent to one or a plurality of sample wells of abiological sample storage device, wherein said biological sample storagedevice comprises (i) a lid, (ii) a sample plate comprising one or aplurality of sample wells that are capable of containing a biologicalsample, and (iii) at least one radio frequency transponder device; and(b) drying one or more of the sample wells, and thereby preparing thebiological sample storage device. In certain further embodiments thestep of administering comprises administering a liquid solution or aliquid suspension that contains the matrix material and the solvent,while in certain other further embodiments at least one well comprisesat least one detectable indicator, while in certain other furtherembodiments at least one well comprises at least one inhibitor that is abiological inhibitor or a biochemical inhibitor.

In another embodiment there is provided a method of recovering a storedbiological sample, comprising (a) contacting, simultaneously orsequentially and in either order in a biological sample storage device,one or a plurality of biological samples with a matrix material, saidbiological sample storage device comprising (i) a lid, (ii) a sampleplate comprising one or a plurality of sample wells that are capable ofcontaining the biological sample, wherein one or more of said wellscomprises the matrix material and wherein the matrix material dissolvesor dissociates in a first solvent, and (iii) at least one radiofrequency transponder device; (b) drying one or more of the samplewells; (c) maintaining the biological sample storage device withoutrefrigeration subsequent to the steps of contacting and drying; and (d)resuspending or redissolving the biological sample in a second solvent,and therefrom recovering the stored biological sample, wherein in acertain further embodiment biological activity of the sample subsequentto the step of maintaining is substantially the same as biologicalactivity of the sample prior to the step of contacting, while in adifferent further embodiment the second solvent is selected from (i) asolvent that is the same as the first solvent and (ii) a solvent that isdifferent from the first solvent. In a certain related embodiment, atleast one of the first solvent and the second solvent is an activitybuffer.

In another embodiment the present invention provides a system forprocessing data regarding the storage, organization, tracking,retrieval, and analysis of biological samples, the system comprising: abiological sample device; a computer-implemented system for receivingand transmitting data regarding the sample device; and a radio frequencyinterface between the sample device and the computer-implemented systemfor providing a communication link between the computer-implementedsystem and the sample device. In a further embodiment thecomputer-implemented system comprises a data structure for maintainingdata regarding the storage, organization, tracking, retrieval, andanalysis of biological samples associated with the sample device. In arelated embodiment the radio frequency interface comprises a radiofrequency interrogator coupled to the computer-implemented system and atleast one transponder device associated with the sample device for radiofrequency communication with the interrogator.

In another embodiment there is provided a method for processing dataregarding the storage, organization, tracking, retrieval, and analysisof biological samples, the method comprising: providing a sample devicefor storing one or more biological samples; providing acomputer-implemented system for receiving, storing, and transmittingdata regarding the sample device or the biological sample or both;providing a radio frequency communication interface between the sampledevice and the computer-implemented system. In a further embodiment themethod comprises generating control signals from thecomputer-implemented system to cause the radio frequency interface toretrieve data from the sample device, and in a distinct furtherembodiment the method comprises generating control signals by thecomputer-implemented system to transmit data to the sample device viathe radio frequency interface.

According to another embodiment, the invention provides a system forprocessing data regarding the storage, organization, tracking,retrieval, and analysis of biological samples, the system comprising abiological sample storage device, said sample storage device comprisinga lid; a sample plate comprising one or a plurality of sample wells thatare capable of containing a biological sample; and at least one radiofrequency transponder device; a computer-implemented system forreceiving and transmitting data regarding the sample storage device; anda radio frequency interface between the sample device and thecomputer-implemented system for providing a communication link betweenthe computer-implemented system and the sample device. In certainfurther embodiments the computer-implemented system comprises a 3-tierarchitecture having a web browser, a web server program, and a databaseserver, and a client-side application that controls operation of theradio frequency interface, and in certain still further embodiments thesystem comprises a USB interface between the web browser and an RFIDreader. In another related embodiment the computer-implemented systemcomprises a 2-tier architecture having an Excel macro program on aclient side and a database server. In another related embodiment thecomputer-implemented system comprises a 2-tier architecture having astand-alone client application and a database server in communicationwith the client application. In certain further embodiments the clientapplication is a compiled application.

In another embodiment, the present invention provides a biologicalsample storage device for one or a plurality of biological samples,comprising (a) a lid (b) a sample plate comprising one or a plurality ofsample wells that are capable of containing a biological sample; and (c)at least one radio frequency transponder device. In a further embodimentthe biological sample storage device comprises a closure means forclosing the lid onto the sample plate, and in certain furtherembodiments the closure means comprises a magnetic closure. In anotherembodiment the biological sample storage device which comprises anairtight closure joint, and in another embodiment the storage devicecomprises an airtight closure joint around each well. In anotherembodiment the biological sample storage device comprises a magneticclosure and an airtight closure joint around each well.

These and other aspects of the present invention will become apparentupon reference to the following detailed description and attacheddrawings. All references disclosed herein are hereby incorporated byreference in their entirety as if each was incorporated individually.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic diagram of a sample plate for dry storage ofbiological materials.

FIG. 2 is a schematic diagram of the air pressure unit and itsinterlocking modules.

FIG. 3 is a schematic diagram of the air pressure unit's air channels.

FIG. 4 is a schematic diagram of the air pressure unit and itsregulation air valve.

FIG. 5 is a schematic diagram of a portable PCR device to providereagents for a sample plate.

FIG. 6 is a schematic diagram of the shipping sleeve.

FIG. 7 is a schematic diagram of the stacking rack.

FIG. 8 is a schematic diagram of the sample storage strip well plate.

FIG. 9 is a schematic diagram of a known radio-frequency communicationsystem.

FIG. 10 is a schematic diagram of a system formed in accordance with oneembodiment of the present invention.

FIG. 11 is a block diagram of a computer-implemented system architectureformed in accordance with another aspect of the present invention.

FIG. 12 shows a computer-implemented system architecture in accordancewith certain invention embodiments.

FIG. 13 shows a computer-implemented system architecture in accordancewith certain invention embodiments.

FIG. 14 shows a gel with PCR products of Deep Vent™ Polymerase. DeepVent™ polymerase was stored at ambient temperature (D) and was hydratedfor either 60 minutes (D 60′) or 5 minutes (D 5′) in the presence ofreaction buffer, template, dNTPs and primers. A frozen stored Deep Ventpolymerase (F) was used as a control. The arrow indicates the PCRproduct of expected size.

FIG. 15 shows (A) length of read (number of bases) for PCR reactionproducts amplified using Big Dye™ enzyme stored frozen, and stored dryon a dissolvable matrix at ambient temperature; and (B) cycle sequencingresults.

FIG. 16 shows HIV protease kinetics after dry storage on a dissolvablematrix.

FIG. 17 shows FIV protease activity after dry storage on a dissolvablematrix.

FIG. 18 shows HIV protease activity after dry storage.

FIG. 19 shows E. coli transformation rate after dry storage on adissolvable matrix.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to a multi-component system and method forthe isolation, purification, preservation, storage, tracking, retrieval,data matching, monitoring and/or analysis of biological samples andbiological materials, minerals and chemicals as described herein. Theinvention may be used for storage of dry samples and for storage atambient temperature, and also may have use for the storage of diversebiological materials and samples, such as but not limited to DNA, RNA,blood, urine, other biological fluids (e.g., serum, serosal fluids,plasma, lymph, cerebrospinal fluid, saliva, mucosal secretions of thesecretory tissues and organs, vaginal secretions, ascites fluids, fluidsof the pleural, pericardial, peritoneal, abdominal and other bodycavities, cell and organ culture medium including cell or organconditioned medium, lavage fluids and the like, etc.) buccal swabs,bacteria, viruses, PCR products, cloned DNA, proteins, cells andtissues, or other biological samples. Biological samples may thereforeinclude a blood sample, biopsy specimen, tissue explant, organ culture,biological fluid or any other tissue or cell preparation, or fraction orderivative thereof or isolated therefrom, from a subject or a biologicalsource. The subject or biological source may be a human or non-humananimal, a primary cell culture or culture adapted cell line includingbut not limited to genetically engineered cell lines that may containchromosomally integrated or episomal recombinant nucleic acid sequences,immortalized or immortalizable cell lines, somatic cell hybrid celllines, differentiated or differentiatable cell lines, transformed celllines and the like.

In certain embodiments, the invention thus relates to the longtermstorage of biological, chemical and biochemical material under dryconditions, and in a manner ready for immediate use after hydration(e.g., upon rehydration). As described herein, there are providedembodiments which include a) the specific dissolvable (or dissociatable)storage matrix, b) preparation and optimization of the storage matrixwith chemicals that increase the durability of the longterm storageconditions, c) preparation of different biological materials prior tothe drying process that allow immediate activity and usability of thematerials after hydration, and d) the process of simplifying complexbiochemical processes through the use of dry stored biologically activematerials. These and related embodiments thus provide surprisingadvantages associated with unrefrigerated dry storage of biologicals,including improved stabilization and preservation of biological activityin biological samples, reduced degradation of biological samples duringstorage at room temperature in dried form (and in particular through theuse of a protective matrix), and simplification of the processes forpreparing biological samples for further use by reducing or eliminatingthe need for time-consuming re-calibration and aliquoting of suchsamples.

The invention allows for purification and size fractionation of DNA,RNA, cells, cellular components and other biological materials,minerals, chemicals, or compositions derived from a biological sample orother life sciences related sample. The invention thus readily permits,for example, the use of one or a plurality of biological materialsand/or biological samples in the performance of molecular biologyprocedures, including but not limited to PCR, biopolymer (e.g.,polynucleotide, polypeptide, or other biopolymer) sequencing,oligonucleotide primer extension, haplotyping (e.g., DNA haplotyping)and restriction mapping in one unified, integrated and easy-to-useplatform. The invention also readily permits, for example and in certainembodiments, the use of one or a plurality of biological samples and/orbiological materials for the performance of protein crystallography. Inother embodiments there is provided a platform for use, testing ordetection (including diagnostic applications) of an antibody or smallmolecule (whether naturally occurring or artificial) or other biologicalmolecule, for example, a protein, polypeptide, peptide, amino acid, orderivative thereof; a lipid, fatty acid or the like, or derivativethereof; a carbohydrate, saccharide or the like or derivative thereof, anucleic acid, nucleotide, nucleoside, purine, pyrimidine or relatedmolecule, or derivative thereof, or the like; or another biologicalmolecule that is a constituent of a biological sample.

The Biological Sample Storage Device

The biological sample storage device (“storage device”) of the presentinvention is comprised of a sample plate and a lid. The dimensions ofthe storage device may be from about 2 mm to about 25 mm in height,about 80 mm to about 200 mm in length, and about 60 mm to about 150 mmin width. Preferably, the storage device has a height of about 3 mm toabout 15 mm, a length of about 100 mm to about 140 mm, and a width ofabout 60 mm to about 100 mm. The storage device may be made out ofcolorful polypropylene and may hold as many as 96, 384, 1536 or moresample deposit wells. Each storage device has its own tight sealing lid.The storage device may be manufactured by injection molding and can bemade in one piece or in multiple pieces.

In preferred embodiments and as described herein, the biological samplestorage device is configured for use in a system for processing sampledata that comprises a radio frequency interface between the storagedevice and a computer-implemented system for receiving, storing and/ortransmitting data. The data may pertain to the storage device and/or tothe one or more biological samples contained therein. According tocertain related embodiments, therefore, the biological sample storagedevice comprises at least one radio frequency transponder device asdescribed herein, which may be an integral component of the storagedevice and/or may be affixed to an interior or exterior surface of thestorage device. Additionally or alternatively, the storage device may bebarcode labeled, and/or may optionally contain one or more fields forcoding using non-erasable marker pens, and/or may optionally include animprinted handling protocol. The plastic material of the sample platemay be about 1/10 of a mm to about 2 mm thick, transmits heat instantly,and is heat resistant up to about 100° C.

The sample plate contains holding areas or wells with a footprint thatis preferably round in shape but can also be square, rectangular,oblong, or of any other shape. The bottom portion of the wells can beflat, conical, cylindrical or round in shape or of any other shape. Theedges of the wells can be of cylindrical, conical or other shape. Thenumber of wells can be as low as 1 well per sample plate and as many asseveral thousand. Most preferably there are about 96 to about 384 wellslocated in the sample plate. The sample wells can also be split intogroups of 1, 4, and 8 wells that can be fit into the standard sampleplate described here. The wells are arranged on the plates in rows. Forthe plates with 96 wells one row contains 8 wells. A unique aspect isthat the sample plate can be a tray that accepts a number of individualsample slides having a varied plurality of wells. Each slide fits intothe tray and allows for the storage of a varied number of wells in asingle plate. The lower surface of the wells is thin, preferably with athickness of about 1/10 of a mm to about 2 mm.

It is contemplated that the present invention will be of major value inhigh throughput screening; i.e., in automated testing or screening of alarge number of biological samples. It has particular value, forexample, in screening synthetic or natural product libraries for activecompounds. The apparatus and methods of the present invention aretherefore amenable to automated, cost-effective high throughputbiological sample testing or drug screening and have immediateapplication in a broad range of pharmaceutical drug developmentprograms. In a preferred embodiment of the invention, the wells areorganized in a high throughput screening format such as a 96-well plateformat, or other regular two dimensional array, such as a 1536- or384-well format. For high throughput screening the format is thereforepreferably amenable to automation. It is preferred, for example, that anautomated apparatus for use according to high throughput screeningembodiments of the present invention is under the control of a computeror other programmable controller. The controller can continuouslymonitor the results of each step of the process, and can automaticallyalter the testing paradigm in response to those results.

Typically, and in certain preferred embodiments such as for highthroughput drug screening, candidate agents are provided as “libraries”or collections of compounds, compositions or molecules. Such moleculestypically include compounds known in the art as “small molecules” andhaving molecular weights less than 10⁵ daltons, preferably less than 10⁴daltons and still more preferably less than 10³ daltons. Candidateagents further may be provided as members of a combinatorial library,which preferably includes synthetic agents prepared according to aplurality of predetermined chemical reactions performed in a pluralityof reaction vessels, which may be provided as wells in a storage deviceaccording to the present disclosure. For example, various startingcompounds may be prepared employing one or more of solid-phasesynthesis, recorded random mix methodologies and recorded reaction splittechniques that permit a given constituent to traceably undergo aplurality of permutations and/or combinations of reaction conditions.The resulting products comprise a library that can be screened followedby iterative selection and synthesis procedures, such as a syntheticcombinatorial library of peptides (see e.g., PCT/US91/08694 andPCT/US91/04666) or other compositions that may include small moleculesas provided herein (see e.g., PCT/US94/08542, EP 0774464, U.S. Pat. No.5,798,035, U.S. Pat. No. 5,789,172, U.S. Pat. No. 5,751,629). Thosehaving ordinary skill in the art will appreciate that a diverseassortment of such libraries may be prepared according to establishedprocedures using storage devices as described herein, and/or testedusing devices and methods according to the present disclosure. Forexample, members of a library of test compounds can be administered to aplurality of biological samples in each of a plurality of wells in asample storage device for use as a high throughput screening array asprovided herein.

The wells may accommodate a biological sample or a biological materialin the form of either liquid or dry material or both. Solid matrixmaterial, such as but not limited to sponge-like material, silica,silica powder, silica filter paper, absorbent powder, or filter paper orother matrix materials as described herein can be added to the wells andwill allow the introduction of biological materials, according tonon-limiting theory, by absorption, adsorption, specific or non-specificbinding or other mechanism of attachment, including those involvingformation of non-covalent and/or covalent chemical bonds and orintermolecular associative interactions such as hydrophobic and/orhydrophilic interactions, hydrogen bond formation, electrostaticinteractions, and the like. The matrix material may be integrated in theproduction process of the sample plate unit, or attached throughadhesive interactions or wedged into the wells, or later introduced intothe wells prior to, concomitant with, or subsequent to introduction ofone or more biological samples into one or more wells. The rim of thewells may be straight or may contain protruding edges. Protruding edgesmay in certain embodiments retain the material matrix within the wellswith or without adhesive interactions. Liquid storage may be achievedthrough reverse conical shape of the wells with a small opening on thesurface of the bottom plate. A reverse conical shape will retain theliquid within the wells in a spill-proof fashion.

The lid may be either flat or have protrusions that fit into the wellsof the bottom sample plate. The lid and the sample plate close eitherthrough snug fit of the sample plate and the lid, or provide an airtightclosure joint or a cushion of compressible material. The joint mayeither be placed around the perimeter of the sample plate and lid oraround each single well. The joint may be attached to the sample plateor to the lid. Preferably, the joint is located in a rim, or glued tothe lid using an adhesive material. An airtight fit may be achieved byinserting the protrusions from the lid as a precision seal into thesample plate wells.

The sample plate may be connected to the lid through a hinge system,located on one of the sides of the storage unit, but it may also belocated on the two opposite sides. The hinge connects the two units andallows the opening and closing of the storage unit. The device may beproduced out of plastic material, whereas the type of plastic can bedetermined dependent on its application. The hinge or hinges allow forremoval of the lid from the sample plate.

The closure of the lid and the sample plate for the long-term storage ofbiological material may in certain preferred embodiments be achievedthrough magnetic adhesion, although other means for closing the lid ontothe plate may also be employed according to other embodimentscontemplated according to the present disclosure, including, asnon-limiting examples, snaps, seals, adhesives, hooks-and-loops,threading closures, solenoids, frustroconical closures, bayonets, pinchclosures, clasps, and the like, or other closure means. The sample plateand the lid of the storage unit thus, in preferred embodiment, containmagnets that may be in the form of a magnetic sheet or in the form ofsmall magnets located within the sample plate and lid of the storagedevice. The magnetic attraction between the sample plate and lid isstrong enough to allow the tight seal of the storage plate but not sostrong as to prevent easy of opening, or twisting or deforming of thesample plate when the lid is opened. The magnetic closure may be used toattach other devices to the storage unit that allows the processing ofbiological material prior to deposition into the storage unit. Themagnetic attraction of the storage unit may be used to attach thestorage device to additional devices below the unit. The magnetism isthe connecting mechanism of the basic unit to other devices or units.

The storage device preferably comprises at least one identification anddata storage tag such as a radio frequency transponder device or “RFtag”, for use as part of a radio frequency communication interfacebetween the biological sample storage device and thecomputer-implemented systems described herein. Certain embodimentscontemplate inclusion of a plurality of RF tags within or on the storagedevice. The storage device may also, according to certain embodiments,comprise visual recognition parts. The different wells may, forinstance, be numbered and marked through the engraving of numbers andletters onto the sample plate or through application of a printingprocess. Optionally, at least one side of the sample plate may have abarcode attached or engraved on its surface. The lid of the storagedevice may have an area for written notes and comments of any kind. Inaddition, the upper surface of the lid may also have a barcode,duplicating the barcode of the sample plate. Dual barcoding allows forthe unique identification of the biological material and for theassociation of the sample plate and the lid. Multiple RF tags and/ormultiple barcoding sites may provide a security mechanism in case one ofthese identification/data storage devices becomes detached, damaged orotherwise unreadable.

The Dry Storage Device

The dry storage device is an application of the storage device asdescribed in this invention, which contains treated matrix material foruse as a dry storage matrix material such as but not limited tosponge-like material, silica, silica powder, silica filter paper,absorbent powder, cotton, wool, linen, polyester or filter paper, andalso including a matrix material that dissolves or dissociates asdescribed herein, for long-term storage of a biological sample or abiological material, such as but not limited to blood, bacteria, cells,viruses, chemical compounds (whether naturally occurring or artificiallyproduced), plasmid DNA, DNA fragments, oligonucleotides, peptides,fluorogenic substrates, genomic DNA, PCR products, cloned DNA, proteins,RNA, minerals or chemicals. These and related embodiments derive fromthe surprising observation that stable, long-term dry storage ofbiological samples or biological materials may be effected withoutrefrigeration when such samples or materials are loaded onto a suitablematrix material such as those described herein, including a dissolvable(or dissociable) matrix material. Accordingly, the present inventionprovides devices for stable, long-term dry storage of biological samplesat common indoor ambient room temperatures (e.g., typically 20-27° C.but varying as a function of geography, season and physical plant fromabout 15-19° C. to about 28-32° C.) for use in the sample dataprocessing methods and systems described herein.

In preferred embodiments that employ the dry storage device, sampleloading results in dry storage, for example, whereby a liquid sample isabsorbed by, adsorbed to or otherwise entrapped by the matrix materialsuch that after loading no free liquid is readily discernible in or on,or easily dislodged from, the matrix material, and which may in certainother embodiments be a dissolvable matrix material or a dissociablematrix material that may be dried before, during, or after beingcontacted with the sample to provide dry storage. Related preferredembodiments thus involve the use of sample storage devices as describedherein that comprise a matrix material which is capable of dry storageof a biological sample or a biological material without refrigeration,for example, at ambient room temperature. In certain related embodimentsa drying step may be performed to effect loading of the sample onto thematrix material for dry storage, for example by air drying, drying atelevated temperature or by the volatilization of solvent throughexposure of the sample loaded matrix material to reduced atmosphericpressure (e.g., lyophilization or other vacuum drying method) or to agentle flowstream of a compatible gas such as nitrogen. The samples arepreferably stored dry under conditions that stabilize the sample, i.e.,little or no detectable (e.g., with statistical significance)degradation or undesirable chemical or physical modification of thesample occurs, according to criteria that will vary as a factor of thenature of the sample being stored and that will in any event be familiarto those having skill in the relevant art.

Certain embodiments provide compositions and methods for storingbiological material (genomic DNA, plasmid DNA, DNA fragments, RNA,oligonucleotides, proteins, peptides, fluorogenic substances, cells,viruses, chemical compounds, etc.) on a matrix comprised of a materialthat dissolves or dissociates in a solvent that allows complete recoveryor substantial recovery (e.g., recovery of at least 50 percent,preferably at least 60 percent, more preferably at least 70 percent,more preferably at least 80 percent, and typically in more preferredembodiments at least 85 percent, more preferably at least 90 percent,more preferably at least 95 percent, still more preferably greater than97, 98 or 99 percent) of the dried sample material after hydration,rehydration or other solvent reconstitution of the sample. For example,a dissolvable matrix may be capable of being solubilized in a suitablesolvent that can be selected based on the properties of the matrixmaterial and/or of the sample depending on the particular methodologybeing employed and in a manner that permits recovery of one or moredesired structural or functional properties of the sample (e.g.,biological activity). Similarly, as another example, the matrix materialmay dissociate in a solvent and may, but need not, become fullysolubilized, such that a dispersion, suspension, colloid, gel, sap,slurry, syrup, or the like may be obtained.

In certain of these and related embodiments, the first solvent which isused to introduce the matrix material and/or the biological sample tothe biological sample storage device prior to a drying step for drysample storage may be the same as the second solvent that issubsequently used to hydrate, rehydrate, reconstitute or resuspend thedried sample/matrix combination, and in other embodiments the secondsolvent may be different from the first. Criteria for selection of asuitable solvent for dissolving or dissociating the matrix materialand/or the biological sample will be known to those familiar with therelevant art based, for example, on physicochemical properties of theparticular matrix material and sample being used, and on the structuralor functional properties (e.g., bioactivity) that are desirably retainedduring dry storage and subsequent reconstitution, as well as on otherfactors (e.g., compatibility with other storage device materials, orliquid handling equipment, safety, etc.). Solvents may be selected, forinstance, based on the solvent polarity/polarizability (SPP) scale valueusing the system of Catalan et al. (e.g., 1995 Liebigs Ann. 241; seealso Catalan, 2001 In: Handbook of Solvents, Wypych (Ed.), Andrew Publ.,NY, and references cited therein), according to which, for example,water has a SPP value of 0.962, toluene a SPP value of 0.655, and2-propanol a SPP value of 0.848. Methods for determining the SPP valueof a solvent based on ultraviolet measurements of the2-N,N-dimethyl-7-nitrofluorene/2-fluoro-7-nitrofluorene probe/homomorphpair have been described (Catalan et al., 1995). Solvents with desiredSPP values (whether as pure single-component solvents or as solventmixtures of two, three, four or more solvents; for solvent miscibilitysee, e.g., Godfrey 1972 Chem. Technol. 2:359) based on the solubilityproperties of a particular matrix material can be readily identified bythose having familiarity with the art in view of the instant disclosure.

According to non-limiting theory, the dissolvable or dissociable matrixmaterial may therefore be a polymer structure that, by forming a matrix,creates a three dimensional space which allows biological material ofthe biological sample to associate with the matrix. The dissolvable ordissociable matrix material may be used to introduce stabilizing agentssuch as salts and buffers under dehydrated (e.g., dried or substantiallysolvent-free) conditions. The matrix also allows the adjustment of pHand other parameters for optimal drying and storage conditions, and maycomprise one or a plurality of detectable indicators as provided herein,such as color-based pH indicators, and/or moisture indicators. Incertain preferred embodiments the matrix material comprises polyvinylalcohol (PVA), a dissolvable matrix material.

According to certain other embodiments, the dissolvable or dissociablematrix material may be any suitable material having the compatiblecharacteristics for storing a particular type of biological sample in amanner that satisfactorily preserves the desired structural and/orfunctional properties, said characteristics including the ability to dryin a manner that forms a matrix within the interstices of which thebiological molecules of interest are deposited, and also includingappropriate solvent (e.g., biological buffer) compatibility furtherincluding an ability to be redissolved or resuspended subsequent to drystorage in a manner whereby the matrix molecules do not interfere withone or more biological activities of interest in the sample. Additionalnon-limiting examples of a matrix material that dissolves or dissociatesin a solvent include polyethylene glycol, agarose,poly-N-vinylacetamide, polyvinylpyrrolidone, poly(4-vinylpyridine),polyphenylene oxide, reversibly crosslinked acrylamide,polymethacrylate, carbon nanotubes (e.g., Dyke et al., 2003 JACS125:1156; Mitchell et al., 2002 Macromolecules 35:8825; Dagani, 2003C&EN 81:5), polylactide, lactide/glycolide copolymer,hydroxymethacrylate copolymer, calcium pectinate, hydroxypropylmethylcellulose acetate succinate (e.g., Langer, 1990 Science 249:1527;Langer, 1993 Accounts Chem. Res. 26:537-542), heparin sulfateproteoglycan, hyaluronic acid, glucuronic acid (e.g., Kirn-Safran etal., 2004 Birth Defects Res. C. Embryo Today 72:69-88), thrombospondin-1N-terminal heparin-binding domain (e.g., Elzie et al., 2004 Int. J.Biochem. Cell Biol. 36:1090; Pavlov et al., 2004 Birth Defects Res. C.Embryo Today 72:12-24), fibronectin (e.g., Wierzbicka-Patynowski et al.,2003 J Cell Sci. 116(Pt 16):3269-76), a peptide/water-soluble polymericmodifier conjugate (e.g., Yamamoto et al., 2002 Curr Drug Targets3(2):123-30), and collagen or collagen fragments including basementmembrane collagen peptides (e.g., Ortega et al., 2002 J Cell Sci. 115(Pt22):4201-14).

Other detectable indicators include compositions that permit detection(e.g., with statistical significance relative to an appropriate control,as will be know to the skilled artisan) or similar determination of anydetectable parameter that directly relates to a condition, process,pathway, induction, activation, inhibition, regulation, dynamicstructure, state, contamination, degradation or other activity orfunctional or structural change in a biological sample, including butnot limited to altered enzymatic (including proteolytic and/ornucleolytic), respiratory, metabolic, catabolic, binding, catalytic,allosteric, conformational, or other biochemical or biophysical activityin the biological sample, and also including interactions betweenintermediates that may be formed as the result of such activities,including metabolites, catabolites, substrates, precursors, cofactorsand the like.

A wide variety of detectable indicators are known to the art and can beselected for inclusion in the presently disclosed compositions andmethods depending on the particular parameter or parameters that may beof interest for particular biological samples in particular samplestorage applications. Non-limiting examples of parameters that may bedetected by such detectable indicators include detection of the presenceof one or more of an amine, an alcohol, an aldehyde, water, a thiol, asulfide, a nitrite, avidin, biotin, an immunoglobulin, anoligosaccharide, a nucleic acid, a polypeptide, an enzyme, acytoskeletal protein, a reactive oxygen species, a metal ion, pH, Na⁺,K⁺, Cl⁻, a cyanide, a phosphate, selenium, a protease, a nuclease, akinase, a phosphatase, a glycosidase, and a microbial contaminant, andothers.

Examples of a broad range of detectable indicators (includingcalorimetric indicators) that may be selected for specific purposes aredescribed in Haugland, 2002 Handbook of Fluorescent Probes and ResearchProducts—Ninth Ed., Molecular Probes, Eugene, Oreg.; in Mohr, 1999 J.Mater. Chem., 9: 2259-2264; in Suslick et al., 2004 Tetrahedron60:11133-11138; and in U.S. Pat. No. 6,323,039. (See also, e.g., FlukaLaboratory Products Catalog, 2001 Fluka, Milwaukee, Wis.; and Sigma LifeSciences Research Catalog, 2000, Sigma, St. Louis, Mo.) A detectableindicator may be a fluorescent indicator, a luminescent indicator, aphosphorescent indicator, a radiometric indicator, a dye, an enzyme, asubstrate of an enzyme, an energy transfer molecule, or an affinitylabel. In certain preferred embodiments the detectable indicator may beone or more of phenol red, ethidium bromide, a DNA polymerase, arestriction endonuclease (e.g., a restriction enzyme used as arestriction nuclease such as a site- or sequence-specific restrictionendonuclease), cobalt chloride (a moisture indicator that changes fromblue color when water is present to pink when dry), Reichardt's dye(Aldrich Chemical) and a fluorogenic protease substrate.

A detectable indicator in certain embodiments may comprise apolynucleotide polymerase and/or a suitable oligonucleotide, either orboth of which may be employed as an indicator or, in certain otherembodiments, as components of other nucleic acids-based applications ofthe compositions and methods described herein. Polymerases (includingDNA polymerases and RNA polymerases) useful in accordance with certainembodiments of the present invention include, but are not limited to,Thermus thermophilus (Tth) DNA polymerase, Thermus aquaticus (Taq) DNApolymerase, Thermologa neopolitana (Tne) DNA polymerase, Thermotogamaritima (Tma) DNA polymerase, Thermococcus litoralis (Tli or VENT™) DNApolymerase, Pyrococcus furiosus (Pfu) DNA polymerase, DEEPVENT™ DNApolymerase, Pyrococcus woosii (Pwo) DNA polymerase, Bacillussterothermophilus (Bst) DNA polymerase, Bacillus caldophilus (Bca) DNApolymerase, Sulfolobus acidocaldarius (Sac) DNA polymerase, Thermoplasmaacidophilum (Tac) DNA polymerase, Thermus flavus (Tfl/Tub) DNApolymerase, Thermus ruber (Tru) DNA polymerase, Thermus brockianus(DYNAZYME™) DNA polymerase, Methanobacterium thermoautotrophicum (Mth)DNA polymerase, mycobacterium DNA polymerase (Mtb, Mlep), and mutants,and variants and derivatives thereof. RNA polymerases such as T3, T5 andSP6 and mutants, variants and derivatives thereof may also be used inaccordance with the invention.

Polymerases used in accordance with the invention may be any enzyme thatcan synthesize a nucleic acid molecule from a nucleic acid template,typically in the 5′ to 3′ direction. The nucleic acid polymerases usedin the present invention may be mesophilic or thermophilic, and arepreferably thermophilic. Preferred mesophilic DNA polymerases include T7DNA polymerase, T5 DNA polymerase, Klenow fragment DNA polymerase, DNApolymerase III and the like. Preferred thermostable DNA polymerases thatmay be used in the methods of the invention include Taq, Tne, Tma, Pfu,Tfl, Tth, Stoffel fragment, VENT™ and DEEPVENT™ DNA polymerases, andmutants, variants and derivatives thereof (U.S. Pat. No. 5,436,149; U.S.Pat. No. 4,889,818; U.S. Pat. No. 4,965,188; U.S. Pat. No. 5,079,352;U.S. Pat. No. 5,614,365; U.S. Pat. No. 5,374,553; U.S. Pat. No.5,270,179; U.S. Pat. No. 5,047,342; U.S. Pat. No. 5,512,462; WO92/06188; WO 92/06200; WO 96/10640; Barnes, W. M., Gene 112:29-35(1992); Lawyer et al., PCR Meth. Appl. 2:275-287 (1993); Flaman et al.,Nucl. Acids Res. 22(15):3259-3260 (1994)).

Other detectable indicators for use in certain embodiments contemplatedherein include affinity reagents such as antibodies, lectins,immunoglobulin Fc receptor proteins (e.g., Staphylococcus aureas proteinA, protein G or other Fc receptors), avidin, biotin, other ligands,receptors or counter receptors or their analogues or mimetics, and thelike. For such affinity methodologies, reagents for immunometricmeasurements, such as suitably labeled antibodies or lectins, may beprepared including, for example, those labeled with radionuclides, withfluorophores, with affinity tags, with biotin or biotin mimeticsequences or those prepared as antibody-enzyme conjugates (see, e.g.,Weir, D. M., Handbook of Experimental Immunology, 1986, BlackwellScientific, Boston; Scouten, W. H., Methods in Enzymology 135:30-65,1987; Harlow and Lane, Antibodies: A Laboratory Manual, Cold SpringHarbor Laboratory, 1988; Haugland, 2002 Handbook of Fluorescent Probesand Research Products—Ninth Ed., Molecular Probes, Eugene, Oreg.;Scopes, R. K., Protein Purification: Principles and Practice, 1987,Springer-Verlag, NY; Hermanson, G. T. et al., Immobilized AffinityLigand Techniques, 1992, Academic Press, Inc., NY; Luo et al., 1998 J.Biotechnol. 65:225 and references cited therein).

The dissolvable (or dissociable) matrix may be applied to storagecontainers for biological samples, for example, by contacting oradministering a matrix material that dissolves or dissociates in asolvent to one or a plurality of sample wells of a storage device asdescribed herein. For instance, the dissolvable matrix material mayreadily adhere to tubes and plates made of glass or plastic such aspolypropylene, polystyrene or other materials. The dissolvable materialis dried, which may by way of non-limiting illustration be accomplishedby air drying at ambient temperature (typically within the range 20°C.-30° C. such as at 22° C., 23° C., 24° C., 25° C.) and/or at anappropriately elevated temperature, and/or under reduced atmosphericpressure (e.g., partial or full vacuum) and/or under a suitable gasstream such as a stream of filtered air, CO₂ or an inert gas such asnitrogen or other suitable drying gas, or by other drying means. Afterthe step of drying, which may be complete drying (e.g., with statisticalsignificance, all or substantially all detectable solvent has beenremoved) or partial drying, the dissolvable/dissociable matrix materialis ready to accept the biological sample to be stored.

Biological material provided in or derived from a biological sample mayalso be added to the wells or tubes in combination with the storagematrix in liquid form (e.g., by simultaneously contacting the samplewell with the sample and the matrix dissolved or dissociated in asolvent), allowing the drying of the biological material and the matrixmaterial to proceed at the same time. The dissolvable matrix does not,in preferred embodiments, interfere with biochemical reactions such thatpurification steps may not be required to separate the matrix from thebiological sample prior to further processing of the sample, forinstance, prior to performance of biochemical reactions, such as assaysor the like, in the wells of the sample storage device.

The buffer conditions in the dissolvable matrix may be adjusted suchthat greater than at least 90 percent, preferably greater than 95percent, more preferably greater than 96, 97, 98 or 99 percent of thebiological activity (e.g., enzymatic or affinity activity, or structuralintegrity or other biological activity as described herein and known tothe art) of the biological sample is maintained upon solventreconstitution (e.g., rehydration with water), eliminating the need tolaboriously remove the sample from the storage container and transfer itto a reaction buffer in a separate container. Certain such inventionembodiments correspondingly provide the unexpected advantage ofeliminating the need to separately aliquot and/or calibrate certainbiological reagents each time a stored sample is to be assayed.

The dissolvable/dissociable matrix may also be prepared in the samplestorage device in a manner such that one or more wells contain at leastone inhibitor that is a biological inhibitor or a biochemical inhibitor,where such inhibitors include any agent that may desirably be includedto preserve, stabilize, maintain, protect or otherwise contribute to therecovery from the biological sample storage device of a biologicalsample that has substantially the same biological activity as waspresent prior to the step of contacting the sample with the samplestorage device. Accordingly, in certain preferred embodiments thebiological sample storage device comprises at least one inhibitor, forexample, an anti-microbial agent such as (but not limited to) ananti-fungal and/or antibacterial agent capable of suppressing bacterialor fungal growth to inhibit microbial contamination of the wells and thestored sample during longterm storage.

In certain related embodiments the inhibitor may be a reducing agent, analkylating agent, an antimicrobial agent, a kinase inhibitor, aphosphatase inhibitor, a caspase inhibitor, a granzyme inhibitor, a celladhesion inhibitor, a cell division inhibitor, a cell cycle inhibitor, alipid signaling inhibitor and/or a protease inhibitor. Those familiarwith the art will be aware of a wide range of readily availableinhibitors that may be selected depending on the nature of thebiological sample and the particular bioactivity of interest. See, e.g.,Calbiochem® Inhibitor SourceBook™ (2004, EMD Biosciences, La Jolla,Calif.). For antimicrobial agents, see, e.g., Pickering, L K, Ed. 2003Red Book: Report of the Committee on Infectious Diseases, 26^(th)edition. Elk Grove Village, Ill., pp. 695-97.; American Academy ofPediatrics, 1998, Pediatrics, 101(1), supplement; DisinfectionSterilization and Preservation, Seymour S. Block (Ed.), 2001 LippincottWilliams & Wilkins, Philadelphia; Antimicrobial Inhibitors, A. I. Laskinand H. A. Lechevalier, (Eds.), 1988 CRC Press, Boca Raton, Fla.;Principles and Practice of Disinfection, Preservation and Sterilization,A. D. Russell et al., (Eds.), 1999, Blackwell Science, Maiden, Mass.;Antimicrobial/anti-infective materials, S. P. Sawan et al., (Eds.), 2000Technomic Pub. Co., Lancaster, Pa.; Development of novel antimicrobialagents: emerging strategies, K. Lohner, (Ed.), 2001 Wymondham, Norfolk,UK; Conte, J. E. Manual of antibiotics and infectious diseases (9^(th)Ed.), 2001, Lippincott Williams & Wilkins, Philadelphia.

In certain embodiments the inhibitor may be the fungizide validamycin A(Research Products International Corp., Mt. Prospect, Ill., catalog no.V21020), the protease inhibitor TL-3 (Lee et al., 1998 Proc. Nat. Acad.Sci. USA 95:939; Lee et al., 1999 J. Amer. Chem. Soc. 121:1145; Buhleret al., 2001 J. Virol. 75:9502), sodium orthovanadate, sodium fluoride,N-α-tosyl-Phe-chloromethylketone, N-α-tosyl-Lys-chloromethylketone,aprotinin, phenylmethylsulfonyl fluoride or diisopropylfluoro-phosphate.

As described herein, an added advantage of the dissolvable matrix isthat the storage container can be directly used as a reaction chamberafter dissolving the matrix and rehydration of the material. Thestability and activity of proteins in liquid form may be dependent onactivity requirements such as pH, salt concentration, and cofactors. Thestability of many proteins may in some cases be extremely labile athigher temperatures and the drying of proteins at ambient (e.g., room)temperature may therefore provide a stabilizing environment.

As also described herein in the Examples, the presence of trehalose,believed to contribute to the stabilization of biological samples (e.g.,Garcia de Castro et al., 2000 Appl. Environ. Microbiol. 66:4142;Manzanera et al., 2002 Appl. Environ. Microbiol. 68:4328), was notsufficient under certain conditions to support recovery of enzymaticactivity in a protein following dry storage. As a brief background,trehalose is the natural substrate of trehalase, an enzyme that cleavesdisaccharides. Trehalose is known to stabilize organic material such asproteins, but when present under suboptimal conditions may bedisadvantageous for longterm storage of proteins at ambienttemperatures, since it is a natural energy source for fungi andbacteria. Contamination with bacteria or fungi of a biological samplestored in the presence of trehalose at less than optimal dry storageconditions will result in growth of the microbe(s), and undesirablemicrobial contamination of the stored sample can result. Validamycin isa trehalase inhibitor having a slightly different chemical structurethan that of trehalose. Validamycin is a non-toxic fungicide thatinhibits fungal growth by blocking the enzyme activity of trehalase.Surprisingly and as disclosed herein and in the Examples, validamycin Ais able to stabilize biological material at ambient temperatures. Inaddition to the protective effect for long-term storage of biologicalmaterial, validamycin also protects the stored sample from contaminationfrom microorganisms.

Accordingly, certain embodiments of the invention expressly contemplatea biological sample storage device that does not include trehalose as acomponent of a sample well or of a matrix material, and similarlycertain embodiments may expressly exclude from the sample well or matrixmaterial the presence of polystyrene and/or of hydroxyectoine. In view,however, of the unexpected advantages disclosed herein as they relate tothe inclusion of validamycin (e.g., validamycin A) as an inhibitor inbiological sample storage devices, certain other embodimentscontemplated herein may include any one or more of trehalose,hydroxyectoine, and/or polystyrene. According to non-limiting theory,validamycin A, a trehalase inhibitor known to the agricultural art as afungicide, provides a surprising stabilizing effect when used incombination with a dissolvable matrix in the biological sample storagedevices, as disclosed herein. Alternatively or additionally to the usedisclosed herein of validamycin along with the dissolvable matrix, othersmall molecules that have activity as inhibitors or activators oftrehalase may be usefully included in the storage devices, as inhibitorsor as additives to the matrix material and/or to the sample, includingnatural disaccharides, pseudo-sugars that are also known ascarba-sugars, and/or other inhibitors/activators of trehalase. Inaddition, validamycin provides an advantage according to certainembodiments disclosed herein, in that it protects the longterm storagemedia from fungal, bacterial or other types of contamination.

Other non-limiting examples of matrix materials that may be used as drystorage matrix materials include materials that comprise one or more ofpolycarbonate, cellulose (e.g., cellulose papers such as FTA™ paper,Whatman Corp., Florham Park, N.J.), cellulose acetate, cellulosenitrate, nitrocellulose, agarose, crosslinked agarose such as2,3-dibromopropanol-crosslinked agarose, 3,6-anhydro-L-galactose,dextrans and other polysaccharides including chemically crosslinkedpolysaccharides such as epichlorohydrin-crosslinked dextran orN,N′-methylene bisacrylamide-crosslinked dextran, borosilicatemicrofiber glass, fiberglass, asbestos, polymers and plastics such aspolypropylene, polystyrene, polyvinylidene fluoride (PVDF), nylon,polysulfone, polyethersulfone, polytetrafluoroethylene, and derivativesof these materials (e.g., U.S. Pat. No. 5,496,562) as well as othersimilar materials as are known in the art, or as can readily bedetermined to be suitable for use in the devices and methods describedherein based on the present disclosure. See also, for example, U.S. Pat.No. 5,089,407, U.S. Pat. No. 4,891,319, U.S. Pat. No. 4,806,343, andU.S. Pat. No. 6,610,531.

The matrix material may be treated for the storage and preservation ofbiological materials. It is well documented that the adjustment ofbuffer conditions and the addition of chemicals and enzymes and otherreagents can stabilize DNA and RNA (for example, Sambrook et al., 1989;Current Protocols, Nucleic Acid Chemistry, Molecular Biology, Wiley andSons, 2003) and proteins and other biological materials (for example,blood, tissue, bodily fluids) against degradation from enzymes,proteases and environmental factors (for example, Current Protocols,Protein Sciences, Cell Biology, Wiley and Sons, 2003). A method thatcombines certain chemical components and beneficial effects may beapplied. Various chemical components may include but are not limited tosodium dodecyl sulfate (SDS), diethyl pyrocarbonate, Tris buffer,Tris-EDTA buffer (TE), sodium chloride/sodium citrate buffer (SSC),MOPS/sodium acetate/EDTA buffer (MOPS), ethylenediamine tetraacetic acid(EDTA), sodium acetate buffer at physiological pH, Guanidiniumthiocyanate, ethylenediamine tetraacetic acid (EDTA), human placentalribonuclease inhibitor, a bovine ribonuclease inhibitor, a porcineribonuclease inhibitor, diethyl pyrocarbonate, ethanol, formamide,guanidinium thiocyanate, vanadyl-ribonucleoside complexes, macaloid,ethylenediamine tetraacetic acid (EDTA), proteinase K, heparin,hydroxylamine-oxygen-cupric ion, bentonite, ammonium sulfate,dithiothreitol (DTT), beta-mercaptoethanol or specific inhibitingantibodies.

Each well holds about 5 μl to about 100 μl of liquid sample material,preferably about 10 μl to about 30 μl of liquid sample material. Sampleamounts can vary from about 0.01 μg to about 1000 μg of DNA, RNA,protein, blood, urine, virus, bacteria, cells, tissue, cell extract,tissue extract, metabolites, chemicals, or other materials. Sampleapplication is through direct spotting and can be automated. The spottedwells may be provided with a color indicator that changes colorindicating an occupied well. Color change may be achieved by adding acolor agent. For example, ponco red dye, Nitrazine yellow, Brom ThymolBlue, Bromocresol Green, Methyl Orange, Congo red, Bromochlorophenol canbe deposited with or prior to subsequent to the sample material, or bytreating the matrix material before or after deposition of samplematerial into the well. A pH-dependent color reagent can be applied thatchanges color after deposition of a sample with a biological pH of 6.5to 8.5 onto the matrix within the well. Spotted wells dry within about 1to about 20 minutes at ambient temperature or within about 0.1 to about10 minutes at elevated temperature. DNA can be retrieved throughre-hydration of the well for up to about 50 to about 80 times. There-hydration reagent may be a solution or sample buffer with abiological pH of 6.5-8.5. Tris buffer, Tris-EDTA buffer (TE), sodiumchloride/sodium citrate buffer (SSC), MOPS/sodium acetate/EDTA buffer(MOPS, sodium acetate buffer. The dry storage device design isapplicable without further modifications for the storage of purifiedgenomic DNA from bacterial, yeast, human, animals, plants and othersources. With additional modification, such as but not limited tocoating the filters with denaturing agents for proteases, the drystorage device can be also used for bacteria, buccal swabs, biopsytissue, semen, urine, blood, proteins and other samples.

Related embodiments are directed to kits that comprise the biologicalsample storage device as described herein, along with one or moreancillary reagents that may be selected for desired uses. Optionally thekit may also include a box, case, jar, drum, drawer, cabinet, carton,carrier, handle, rack, tray, pan, tank, bag, envelope, sleeve, housingor the like, such as any other suitable container. Ancillary reagentsmay include one or more solvents or buffers as described herein andknown to the art, and may in certain embodiments include an activitybuffer.

An activity buffer may comprise a solvent or solution in liquid form,including a concentrate, or one or more dry ingredients which, whenreconstituted with, dissolved in and/or diluted with one or moreappropriate solvents (e.g., water typically, or alternatively, analcohol such as methanol, ethanol, n-propanol, isopropanol, butanol,etc., an organic solvent such as dimethylsulfoxide, acetonitrile,phenol, chloroform, etc. or other solvent) as appropriate for theintended use, results in a liquid that is suitable for a desired use ofthe biological sample, such as a functional or structuralcharacterization of one or more components of the sample.

Non-limiting examples of such uses may include determining one or moreenzyme activities, determining intermolecular binding interactions,detecting the presence of a specific polynucleotide or amino acidsequence or of an immunologically defined epitope or of a definedoligosaccharide structure, detection of particular viruses or ofmicrobial cells or of human or animal cells, determining particularmetabolites or catabolites, etc., all of which can be accomplished usingconditions that are defined and known to those skilled in the relevantart, including suitable conditions that can be provided throughcontacting the sample with an appropriate activity buffer.

The Wet Storage Device

The storage device can be modified for wet storage of samples throughone or more changes to the well design. Cross-contamination across wellsthrough spillage while opening and closing of the wells is avoided by adesign that provides a small opening on the top part of the well whileretaining the liquid in the well through surface tension.

The small opening on the top part of the well may be provided through areverse cone design or through plastic flaps protruding from the top ofthe well into the open space reducing the overall opening of each well.The wet storage device is manufactured by injection molding and can bemade in one piece or in two pieces similar to the storage device. Thewet storage device withstands temperatures ranging from about −80° C. toabout 100° C.

Strip Well Module

All devices and applications described in this invention may be used ina strip well format with either 1, 4 or 8 well strips. The strip wellmodule has the same or similar basic footprint as the storage device. Itallows the storage of smaller sample numbers than the 96 well plateunit. The modular design allows the attachment of well strips to a thinbase platform. One strip can either contain 1, 4 or 8 wells. The stripscan be attached to a thin base-plate either through magneticinteractions or through clips present at the end of the strips Theheight of one strip, including the thickness of the base-plate, is equalto a regular basic storage unit, so that the lid of the unit allows forthe closing of the device.

The Pressure Device

The Pressure Device of the present invention is comprised of severalmodules, which include the previously described sample storage device, afilter unit, a pressure plate unit, and a pressurized air system. Allunits are of equal dimension, equivalent to a standard 96-well, 384-wellor 1535-well biological sample plate. The dimensions of the pressuredevice are about 2 mm to about 25 mm in height, 80 mm to 200 mm inlength, and about 60 mm to about 150 mm in width. Preferably, thepressure device has a height of about 3 mm to about 20 mm, a length ofabout 100 mm to about 140 mm, and a width of about 60 mm to about 100mm, but can also have smaller dimensions to accommodate small samplenumbers, or smaller sample systems. All modules may vary in dimensiondependant on the size of the sample storage device dimension, whereasthe number of wells can be as low as 1 well per sample plate and as manyas tens of thousands. Most preferably 96 or 384 wells may be provided inthe sample plate and processed through each of the pressure plate units.The number of sample wells of each pressure device can also be splitinto groups of 1, 4 and 8 wells that can be fit into the standard sampledevice described in this invention. The pressure device is made out ofcolorful plastic material or out of, metal or of combinations of both.The body of the pressure device and its modules is made by injectionmolding or machine tooling or a combination of both.

The filter unit may be attached to the pressure device and the samplestorage device and any other devices described herein by magneticforces. An additional clasp may be provided to aid in withstanding airpressure during operation. The filter unit may be made out of colorfulsolid material such as polypropylene, acrylic, and contains paper or asolid matrix for filtration. Preferably, the filter unit has a thicknessof about 1 mm to about 15 mm depending on the substrate used forfiltration. The filter unit has the appropriate number of holes/slotsthat fit over a sample storage device and holds 96, 384, 1536 or moresample deposit holes. Each filter unit has its own tight sealing lid.The rim of the holes can be either straight or can contain protrudingedges. Protruding edges can retain the matrix material within the holeswith or without adhesive interactions.

Each hole within the filter unit may contain matrix materials, such asbut not limited to sponge-like material, silica, absorbent powder, andfilter paper for the filtration of biological materials, such as but notlimited to blood, bacteria, genomic DNA, mitochondrial DNA, PCRproducts, cloned DNA, proteins, RNA, proteins, minerals or chemicals.The matrices may be selected to support biological sample processing,for example by way of illustration and not limitation, one or more ofDNA purification, PCR amplification, sample size fractionation (e.g., onthe basis of molecular size or cell size), serum processing, bloodprocessing, protein purification and cell sorting. The matrix materialsmay be either integrated in the production process of the sample plateunit, or attached through adhesive interactions or wedged into theholes. The matrices are prepared using standard technology necessary tomake size fractionation filters, or treated material to degrade orretain unwanted biological fractions (for example, Current Protocols,Molecular Biology, Wiley and Sons, 2003). The matrix materials may alsobe treated with antibodies, lectins, or other affinity,charge-selective, ion selective, group selective (e.g., amino orcarboxyl functionalities), hydrophobic, hydrophilic or other selectivitymolecules or the like to retain fractions of the sample material, and/orwith small chemical entities conferring desired biological or chemicalfunctions or functionalities (see, for example, Current Protocols inMolecular Biology, John Wiley and Sons, 2003; Scopes, R. K., ProteinPurification: Principles and Practice, 1987, Springer-Verlag, NY; Weir,D. M., Handbook of Experimental Immunology, 1986, Blackwell Scientific,Boston; and Hermanson, G. T. et al., Immobilized Affinity LigandTechniques, 1992, Academic Press, Inc., California). The matrixmaterials may be pretreated to preserve the biological material byregulation of buffer conditions and by modification of chemicaladditives, stabilizers or degradation reagents (for example, Sambrook etal., 1989; Current Protocols, Nucleic Acid Chemistry, Protein Science,Molecular Biology, Cell Biology, Wiley and Sons, 2003). Each hole mayprocess from about 5 μl to about 1000 μl of sample volume. Sampleamounts can vary from about 0.1 μg of DNA to about 1000 μg of DNA, RNA,protein, blood, urine, virus, bacteria, cells, tissue, cell extract,tissue extract, metabolites, chemicals, or other materials. Sampleapplication is through direct spotting and can be automated.

The pressure plate unit applies air pressure from the top to the filterunit holes and forces the sample through the matrices into the well ofthe storage device located below. Pressure may be applied from apressurized laboratory air system or a pressurized air canister. Thepressure unit may be applied to introduce through top pressure thereagents into the wells of the sample storage device, the PCR device,the sequencing device, the restriction analysis device, the proteincrystallography device, the diagnostic device, and the strip welldevice. The pressure plate unit is provided with holes connecting allholes to an air intake. The air intake is attached to a valve that hasan air-tight seal connecting the pressure plate unit to a pressurizedair source. The pressure unit attaches to an air source by turning andsecuring the valve. The valve can also be attached to a pressure gaugeindicating the required pressure for each specific filter unit.

All modules for the pressure device described herein are preferablyairtight to attain a seal that withstands the pressure required to forcethe sample through the filter system into the storage wells. Each modulemay be flat or have protrusions that fit exactly into the adjoiningmodule. An airtight fit is created by use of a joint or a cushion ofcompressible material. The joint may either be placed around theperimeter of each unit or around each single well. Preferably the jointis located in a rim, or affixed to the lid using an adhesive material.An airtight fit may be achieved by inserting the protrusions from eachunit as a precision seal into the unit it will be attached to below.

The attachment of all modules, including a pressure unit, a filter unitand a storage device, is preferably achieved through magnetic adhesion(but may alternatively, in these and other device embodiments whichfollow, employ other closure means as described herein). Each unitcontains magnets either in the form of a magnetic sheet or in the formof small magnets. The magnetic attraction between each unit is strongenough to allow the tight seal for the processing of biological materialprior to deposition into the sample storage or other device. Themagnetic attachment of the three independent modules (pressure unit,filter unit and storage device) may be further secured by clasps. Theclasps may be made of metal or plastic material that is formed to wedgethe three modules together and to reinforce the magnetic attachmentmechanism. The clasp preferably has dimensions smaller than the sides ofthe filtration unit. The clasps may be attached through the applicationof outside pressure that opens the clasp, or the clasps may be designedto slide over the outside of the filter module. Two or more clasps maybe utilized to secure the filter unit.

Each module has visual recognition parts. The different wells maynumbered and marked through the engraving of numbers and letters ontothe sample plate or through application of a printing process.

Portable PCR Device

The sample plate may be attached to a thermocycling unit (PCR device)through magnetic forces. The sample plate and the PCR device containmagnets either in the form of a magnetic sheet or in the form of smallmagnets located inside of the sample plate. The magnetic attractionbetween the sample plate and the PCR device allows for exact placementand tight attachment of the sample plate to the PCR device.

The PCR device contains a temperature platform with the footprint of thestorage device. The PCR device produces temperatures in the range fromabout 4° C. to about 100° C. The PCR device contains a computercomponent that can be programmed for repeated cycling protocols thatcontain multiple temperatures, varied temperature holding times, andmultiple temperature changes that can range from 4° C. to 100° C. andthat accommodate the requirements for standard and hot-start PCRamplification conditions (for example, Qiagen “Taq PCR Handbook”, Qiagen“Critical Factors for Successful PCR”). The PCR unit can contain anintegrated heated lid or cover that sustains and produces constanttemperatures up to about 100° C. The lid or cover may be made out ofmetal or similar material and is placed and held in place via magneticforce on the top of the sample plate. The energy provided for this PCRunit can come from a standard 110/220V electrical outlet, from a batterypack or from a solar driven energy source.

PCR Reagent Module

The PCR reagent module contains all reagents necessary for PCRamplification. It can include reagents such as but not limited tobuffers, primers, polymerase enzyme, and deoxynucleotides (for example,Qiagen “Taq PCR Handbook”, Qiagen “Critical Factors for SuccessfulPCR”). The reagents are provided in a 96, 384, or 1536 well or largerformat which matches the format and dimensions of the sample plate. Thedimensions of the PCR reagent module are about 2 mm to about 25 mm inheight, about 80 mm to about 200 mm in length, and about 60 mm to about150 mm in width. Preferably, the PCR reagent module has a height ofabout 3 mm to about 15 mm, a length of about 100 mm to about 140 mm, anda width of about 60 mm to about 100 mm. The PCR reagent module is madeout of colorful polypropylene and holds 96, 384, 1536 or more sampledeposit wells. The PCR reagent module is manufactured by injectionmolding.

Magnetism is the connecting mechanism of the sample plate to the PCRreagent module. The sample plate and the PCR reagent module containmagnets preferably in the form of a magnetic sheet or in the form ofsmall magnets located inside of the sample plate. The magneticattraction between the sample plate and the PCR reagent module allowsfor exact placement and tight attachment of the sample plate to the PCRreagent module.

The PCR reagent module may have different designs. Each sample well mayor may not have protruding edges that reach into the wells of the sampleplate. It may require application of air pressure applied by thepressure device to transfer the reagents from the PCR reagent moduleinto the sample plate.

Sequencing Reagent Module

The sequencing reagent module contains all reagents necessary for DNAsequencing or DNA cycle sequencing. It can include reagents such as butnot limited to buffers, primers, sequencing enzyme, deoxynucleotides anddideoxynucleotides (for example, Nucleic Acid Chemistry, MolecularBiology, Wiley and Sons, 2003). The reagents are provided in a 96, 384,or 1536 well or larger format, which matches the format and dimensionsof the sample plate. The dimensions of the sequencing reagent module areabout 2 mm to about 25 mm in height, about 80 mm to about 200 mm inlength, and about 60 mm to about 150 mm in width. Preferably, thesequencing reagent module has a height of about 3 mm to about 15 mm, alength of about 100 mm to about 140 mm, and a width of about 60 mm toabout 100 mm. The sequencing reagent module is made out of colorfulpolypropylene and holds 96, 384, 1536 or more sample deposit wells. Thesequencing reagent module is manufactured by injection molding.

Magnetism is the connecting mechanism of the sample plate to thesequencing reagent module. The sample plate and the sequencing reagentmodule contain magnets preferably in the form of a magnetic sheet or inthe form of small magnets located inside of the sample plate. Themagnetic attraction between the sample plate and the sequencing reagentmodule allows for exact placement and tight attachment of the sampleplate to the sequencing reagent module.

The sequencing reagent module may have different designs. Each samplewell may or may not have protruding edges that reach into the wells ofthe sample plate. It may require application of air pressure applied bythe pressure device to transfer the reagents from the sequencing reagentmodule into the sample plate.

Primer Extension Reagent Module

The primer extension reagent module contains all reagents necessary forprimer extension. It can include reagents such as but not limited tobuffers, primers, polymerase enzyme, deoxynucleotides anddideoxynucleotides (for example, Current Protocols, Nucleic AcidChemistry, Molecular Biology, Wiley and Sons, 2003). The reagents areprovided in a 96, 384, or 1536 well or larger format, which matches theformat and dimensions of the sample plate. The dimensions of the primerextension reagent module are about 2 mm to about 25 mm in height, about80 mm to about 200 mm in length, and about 60 mm to about 150 mm inwidth. Preferably, the primer extension reagent module has a height ofabout 3 mm to about 15 mm, a length of about 100 mm to about 140 mm, anda width of about 60 mm to about 100 mm. The primer extension reagentmodule is made out of colorful polypropylene and holds 96, 384, 1536 ormore sample deposit wells. The primer extension reagent module ismanufactured by injection molding.

Magnetism is the connecting mechanism of the sample plate to the primerextension reagent module. The sample plate and the primer extensionreagent module contain magnets preferably in the form of a magneticsheet or in the form of small magnets located inside of the sampleplate. The magnetic attraction between the sample plate and the primerextension reagent module allows for exact a placement and tightattachment of the sample plate to the primer extension reagent module.

The primer extension reagent module may have different designs. Eachsample well may or may not have protruding edges that reach into thewells of the sample plate. It may require application of air pressureapplied by the pressure device to transfer the reagents from the primerextension reagent module into the sample plate.

Haplotyping Reagent Module

The haplotyping reagent module contains all reagents necessary for DNAhaplotyping. It can include reagents such as but not limited to buffers,primers, sequencing enzyme, deoxynucleotides and dideoxynucleotides (forexample, Current Protocols, Nucleic Acid Chemistry, Molecular Biology,Wiley and Sons, 2003). The reagents are provided in a 96, 384, or 1536well or larger format which matches the format and dimensions of thesample plate. The dimensions of the haplotyping reagent module are about2 mm to about 25 mm in height, about 80 mm to about 200 mm in length,and about 60 mm to about 150 mm in width. Preferably, the haplotypingreagent module has a height of about 3 mm to about 15 mm, a length ofabout 100 mm to about 140 mm, and a width of about 60 mm to about 100mm. The haplotyping reagent module is made out of colorful polypropyleneand holds 96, 384, 1536 or more sample deposit wells. The haplotypingreagent module is manufactured by injection molding.

Magnetism is the connecting mechanism of the sample plate to thehaplotyping reagent module. The sample plate and the haplotyping reagentmodule contain magnets preferably in the form of a magnetic sheet or inthe form of small magnets located inside of the sample plate. Themagnetic attraction between the sample plate and the haplotyping reagentmodule allows for exact placement and tight attachment of the sampleplate to the haplotyping reagent module.

The haplotyping reagent module may have different designs. Each samplewell may or may not have protruding edges that reach into the wells ofthe sample plate. It may require application of air pressure applied bythe pressure device to transfer the reagents from the haplotypingreagent module into the sample plate.

Restriction Analysis Reagent Module

The restriction analysis reagent module contains all reagents necessaryfor DNA restriction analysis. It can include reagents such as but notlimited to buffers, restriction enzyme, and salt (for example, Sambrooket al., 1989; Current Protocols, Nucleic Acid Chemistry, MolecularBiology, Wiley and Sons, 2003). The reagents are provided in a 96, 384,or 1536 well or larger format, which matches the format and dimensionsof the sample plate. The dimensions of the restriction analysis reagentmodule are about 2 mm to about 25 mm in height, about 80 mm to about 200mm in length, and about 60 mm to about 150 mm in width. Preferably, therestriction analysis reagent module has a height of about 3 mm to about15 mm, a length of about 100 mm to about 140 mm, and a width of about 60mm to about 100 mm. The restriction analysis reagent module is made outof colorful polypropylene and holds 96, 384, 1536 or more sample depositwells. The restriction analysis reagent module is manufactured byinjection molding.

Magnetism is the connecting mechanism of the sample plate to therestriction analysis reagent module. The sample plate and therestriction analysis reagent module contain magnets preferably in theform of a magnetic sheet or in the form of small magnets located insideof the sample plate. The magnetic attraction between the sample plateand the restriction analysis reagent module allows for exact placementand tight attachment of the sample plate to the restriction analysisreagent module.

The restriction analysis reagent module may have different designs. Eachsample well may or may not have protruding edges that reach into thewells of the sample plate. It may require application of air pressureapplied by the pressure device to transfer the reagents from therestriction analysis reagent module into the sample plate.

Diagnostic Device

The basic sample storage device may be modified to function as ananalytical device used in the detection of hormone levels, physiologicalconditions, human, animal and plant diseases. The diagnostic device mayimplement the placing of a cylindrical diagnostic device on top of thesample storage device. The diagnostic device may be produced in twoways: 1) an independent production process and added as the completedevice into the sample storage device, or 2) layered as independentunits within each well of the sample storage device.

The diagnostic device may contain a zone with at least one specificantibody or specific diagnostic reagent within the device. The reagentsmay produce a visually detectable reaction when an antibody-antigencomplex is formed.

Shipping Sleeve

The shipping sleeve is used to safely transport or mail biologicalmaterial. The shipping sleeve is designed to hold a sample storagedevice and an information storage medium, for example a compact disc(CD) containing the information concerning the material. In cases wheredangerous or infectious materials are shipped the wells can be sealedwith an adhesive film prior to closing of the sample storage device. Theshipping sleeve has two parts, the bottom part or sample storage deviceholder, and the enclosure. The bottom part may be made out of cardboard,plastic or foam material than has the exact footprint of the samplestorage device and a software CD or other information storage medium.For shipment or transport of biological material the sample is spottedinto the wells of the sample storage device, and the lid is closed andsealed through its magnetic lid-closure. The sample storage device isplaced into the tight-fit of the shipping sleeve bottom. The CD may beadded.

The size of the sample storage device holder may be determined by thesize of the sample storage device it may not be smaller than a samplestorage device, but it may be larger than 10 stacked sample storagedevices. The surrounding padding material preferably consists of atleast about 5 mm additional padding and up to about 10 cm. The samplestorage device holder also contains space for a secure fit of aninformation device. The location of the information device holder withinthe transportation sleeve depends on the type of information device. Itis designed to provide a snug fit for either one or multiple CDs ormemory cards/memory sticks. The sample storage device holder is producedpreferably of formable material, such as cardboard or foam based. Thesample storage device holder including the padding material is eithersurrounded by an outside enclosure or is integrated into an enclosuresurrounding the sample storage device(s) and the information storagedevice from all six sides including an opening lid or surrounding thesample storage device holder from 5 sides. In case the sample storagedevice holder includes an opening lid, the lid is attached to one of thesides of the sample storage device holder, covers one of the samplestorage device holder sides and attaches to the opposite side andsecurely closes the transport sleeve. For the 5-sided sample storagedevice holder surrounding the closure of the 6th side is providedthrough a closing box, sliding over the entire sample storage deviceholder. The enclosure can be of package material providing rigidity tothe sample storage device holder. Space is provided on the outside ofthe transport sleeve for address labels and postage stamps.

Protein Crystallography Module

The crystallography module contains wells that may be filled withdifferent protein crystallization solutions and dehydrated. The basicstorage device may be produced out of clear see-through plastic and eachindividual well contains a protein crystallization condition spanningthe pH range from about 4.6 to about 9.4, Each well may containdifferent buffers such as but not limited to acetate, tartrate,phosphate, Tris, citrate, HEPES, imidazole, formate, cacodylate, MES,Bicine, Tris, citrate, HEPES, acetate and different precipitating saltssuch as tartrate, phosphate, ammonium and lithium sulfate, magnesium andcalcium chloride, magnesium, ammonium, sodium, zinc and calcium acetate,sodium citrate, sodium and magnesium formate, magnesium and sodiumchloride, sodium acetate, sodium citrate, ammonium formate, lithium andammonium sulfate, imidazole, CTAB and precipitating organic solventslike MPD, 2-propanol, ethylene glycol, dioxane, ethanol, 1,6-hexanediol.They can also contain PEG 400, 6000, 1000, 8000, 10000, and 20000, PEGMME 550, 2000, 5000, and 2000, Jeffamine M-600 or other additives liketert-butanol, glycerol, Co²⁺, Cd²⁺, Fe³⁺, Ni²⁺, and Zn²⁺ ions, dioxane,ethylene glycol, polyethyleneimine. The wells may be filled with thesolutions above at different concentrations. The wells are dehydrated,retaining the substances on the walls of the wells. The wells are readyto use, can be rehydrated with water and the protein may be added.

Stacking Rack

The individual sample storage units may be stored either at roomtemperature or refrigerated in specially designed storage rack. The rack(see Figures) may hold different amounts of sample storage units, thebarcode is preferably visible and the units may slide easily on plastictracks. The storage rack may be either open or enclosed in a plastic boxwith closing door.

The stacking rack can be produced out of plastic or metal. It may hold10, 25 or 50 sample storage devices. The sample storage devices slide ontracks into the stacking rack. A locking mechanism prevents the cardsfrom falling out of the stacking rack. The stacking rack can be eitheropen or may be completely enclosed by protective material and one hingeddoor at the front side of the stacking rack.

System for Storing, Tracking, and Retrieving Data Associated WithBiological Materials

The foregoing storage device in the various embodiments described abovecan be combined with other technologies to provide for integration ofsample storage and sample management for life science applications. Thisembodiment of the invention enables the integration of biological samplestorage, location, tracking, processing, and sample data management.Data regarding samples can be associated with the location of thesamples through direct physical association of the data with the samplestorage devices. The stored information can be updated with additionaldata that originates from inventory and tracking of samples incombination with multi-step biological research protocols, productionprocesses, screening, bioassays, patient histories, clinical trial data,and other sources of developed information. The data associated with thesample can be transmitted and shared through a secure hierarchicalsoftware and networking architecture that enables interfacing ofmulti-user, multi-site environments.

Ideally, information about a sample is integrated with the samplestorage device by an associated electronic interface, preferably awireless interface, such as a radio frequency identification (RFID)transponder. While barcodes have been used in the past to identifysamples, this technology has limitations that make it unsuitable for usein the present invention. These limitations include the requiredline-of-sight access to the barcode for transfer of information, limitedinformation capacity, and interference through environmental factorssuch as dust, moisture, and the like. Radio frequency identificationtechnology overcomes these disadvantages.

Remote communication utilizing wireless equipment typically relies onradio frequency (RF) technology, which is employed in many industries.One application of RF technology is in locating, identifying, andtracking objects, such as animals, inventory, and vehicles. Examples ofpublications disclosing RF identification tag systems include thedisclosures of U.S. Pat. Nos. 6,696,028; 6,380,858; and 5,315,505.

RF identification (RFID) tag systems have been developed that facilitatemonitoring of remote objects. As shown in FIG. 9, a basic RFID system 10includes two components: an interrogator or reader 12, and a transponder(commonly called an RF tag) 14. The interrogator 12 and RF tag 14include respective antennas 16, 18. In operation, the interrogator 12transmits through its antenna 16 a radio frequency interrogation signal20 to the antenna 18 of the RF tag 14. In response to receiving theinterrogation signal 20, the RF tag 14 produces an amplitude-modulatedresponse signal 22 that is transmitted back to the interrogator 12through the tag antenna 18 by a process known as backscatter.

The conventional RF tag 14 includes an amplitude modulator 24 with aswitch 26, such as a MOS transistor, connected between the tag antenna18 and ground. When the RF tag 14 is activated by the interrogationsignal 20, a driver (not shown) creates a modulating on/off signal 27based on an information code, typically an identification code, storedin a non-volatile memory (not shown) of the RF tag 14. The modulatingsignal 27 is applied to a control terminal of the switch 26, whichcauses the switch 26 to alternately open and close. When the switch 26is open, the tag antenna 18 reflects a portion of the interrogationsignal 20 back to the interrogator 12 as a portion 28 of the responsesignal 22. When the switch 26 is closed, the interrogation signal 20travels through the switch 26 to ground, without being reflected,thereby creating a null portion 29 of the response signal 22. In otherwords, the interrogation signal 20 is amplitude-modulated to produce theresponse signal 22 by alternately reflecting and absorbing theinterrogation signal 20 according to the modulating signal 27, which ischaracteristic of the stored information code. The RF tag 14 could alsobe modified so that the interrogation signal is reflected when theswitch 26 is closed and absorbed when the switch 26 is open. Uponreceiving the response signal 22, the interrogator 12 demodulates theresponse signal 22 to decode the information code represented by theresponse signal. The conventional RFID systems thus operate on a singlefrequency oscillator in which the RF tag 14 modulates a RF carrierfrequency to provide an indication to the interrogator 12 that the RFtag 14 is present.

The substantial advantage of RFID systems is the non-contact,non-line-of-sight capability of the technology. The interrogator 12emits the interrogation signal 20 with a range from one inch to onehundred feet or more, depending upon its power output and the radiofrequency used. Tags can be read through a variety of substances such asodor, fog, ice, paint, dirt, and other visually and environmentallychallenging conditions where bar codes or other optically-readtechnologies would be useless. RF tags can also be read at remarkablespeeds, in most cases responding in less than one hundred milliseconds.

A typical RF tag system 10 often contains a number of RF tags 14 and theinterrogator 12. RF tags are divided into three main categories. Thesecategories are beam-powered passive tags, battery-powered semi-passivetags, and active tags. Each operates in fundamentally different ways.

The beam-powered RF tag is often referred to as a passive device becauseit derives the energy needed for its operation from the interrogationsignal beamed at it. The tag rectifies the field and changes thereflective characteristics of the tag itself, creating a change inreflectivity that is seen at the interrogator. A battery-poweredsemi-passive RF tag operates in a similar fashion, modulating its RFcross-section in order to reflect a delta to the interrogator to developa communication link. Here, the battery is the source of the tag'soperational power. Finally, in the active RF tag, a transmitter is usedto create its own radio frequency energy powered by the battery.

In a preferred embodiment of the present invention, the system consistsof three parts, a consumable hardware device, inventory and managementsoftware, and the RFID interface between the hardware device and thesoftware. Referring to FIG. 10, shown therein is a system 100 formed inaccordance with one embodiment of the invention to include the storagedevice 102 described above, the inventory and management softwarecomponent 104, preferably implemented in a computer system 106, and theradio frequency identification interface 108 coupling the storage device102 and the software 106. Preferably, the RFID interface 108 includes atransponder 100 associated with the storage device 102 and aninterrogator 112, which is coupled to the computer-implemented system106.

In this embodiment, the transponder 110 is associated with the samplestorage device 102, such as by affixing the transponder 110 to anexterior surface of the storage device 102. However, it is to beunderstood that the transponder 110 can be affixed to or associated witha tube, a plate, a rack, or even a room in which the storage device 102is maintained. While it is preferred that a single transponder 110 beassociated with a single storage device 102, it is possible that eachparticular sample stored in the storage device 102 can have atransponder 110 associated with it.

Association can be achieved either during production of the storagedevice 102 such that the transponder 110 is embedded in the storagedevice 102 or after the storage device 102 has been produced, such asthrough adhesive affixation to the storage device 102. Inasmuch asmagnetism is the preferred connecting mechanism used in the samplestorage device 102 in its various embodiments, it will be understood byone of ordinary skill in this technology that appropriate shielding maybe needed to prevent unintentional altering of information stored in thetransponder 110 and to prevent interference with radio frequencycommunications between the transponder 110 and the interrogator 112.

The transponder 110 can be preprogrammed with data about the storagedevice 102 and the samples stored in the storage device 102, includingownership information, location information, analysis information,production processes, clinical trial conduct, synthesis processes,sample collections, and other information known to those skilled in theart that would be of value in managing samples. In addition topreprogramming such data, the transponder 110 can be configured topermit modification and updating of the data within its memory. Inaddition, the transponder 110 will contain security architecture thatdefines precise access conditions per type of data to thereby restrictreading, writing, and updating. For example, the RFID interface 108components can be configured to receive control signals from and torespond to a particular computer-implemented data processing system,such as the software application described herein below. In addition,data written to the transponder 110 can be encrypted for authenticationand security purposes.

The use of RFID transponders or chips offers the benefit of a widetemperature range (−25° C. to +85° C.) without the loss offunctionality. In addition, the transponders 110 can be utilized tocontrol remote devices, such as a signaling light or generator ofaudible tones for alerting and locating the object associated with thetransponder 110. Storage of information in the transponder 110 alsoprovides an additional backup should data in the computer-implementedsystem 106 be damaged or lost.

The interrogator 112 is a conventional radio frequency identificationreader that is coupled to the computer-implemented system 106. Commandand control signals are generated by the system 106 to initiateinterrogation of one or more transponders 110 and to receive a responsetherefrom that is processed by the software 104 in thecomputer-implemented system 106. In one configuration, the transponders110 can be reprogrammed via communications from the interrogator 112 toreplace or update data stored therein.

In one implementation, one or more interrogators 112 are positionedwithin a facility at a sufficient range to communicate via radiofrequency signals, such as microwave signals, with the transponders 110.Multiple interrogators 112 can be used for multiple classes oftransponders 110 or with individual transponders 110. Alternatively, oneinterrogator utilizing known technology can communicate with multipletransponders 110 on multiple frequencies in serial fashion orconcurrently. In applications where a sample storage device 102 orindividual samples are processed, multiple interrogators positioned atvarious locations within a structure or along a path of travel, such asa conveyor system or a shipping system, such as freight lines, trains,and the like, can be used to track the location and the status of thesample. This includes checking environmental factors, such astemperature, humidity, pressure, and the like in which the specimen orstorage device 102 is located.

Thus, the RFID interface 108 can be expanded to monitor and process datarelated to the movement and analysis of a sample or storage device 102located in a laboratory, manipulated by laboratory robots, and the likesuch as during biological production processes or the execution ofexperimental steps. This also aids in quality control and in processingbiological samples through automated or semi-automated researchprotocols.

As mentioned above, sample storage and tracking are facilitated bylocating a sample through the use of an RF interface between the RFtransponder on the sample storage device and the computer-implementedsystem described herein, which is achieved through the tagging andmonitoring of the storage location, such as a storage rack, a storageroom, a refrigerator, a lab bench, a desk, or a bookshelf.

In order to trace a particular storage device 102 or sample, thetransponder 110 is configured to activate a remote device, such as ablinking light located on the storage device, an audible deviceassociated with the storage device, or a color change of the storagedevice that can be recognized by a person or by an automated system, toenable fast retrieval of the sample. In addition, the transponder 110 isconfigured to activate a remote alarm when an environmental conditionhas exceeded a predetermined environmental range, including but notlimited to temperature, pressure, and humidity. In one embodiment, thetransponder 110 is a passive device that is activated by theinterrogation signal, from which it draws operating power. When thetransponder 110 is used to activate a remote device or to increase therange of communication, the transponder can be semi-active as describedabove. Alternatively, an active transponder can be used when largeamounts of data are to be read from or written to the transponder 110 orincreased range as desired. Range is also affected by frequency, as isknown in the art, and one of ordinary skill would select the appropriatefrequency range in accordance with the environment, and the functionalobjectives. For example, certain specimens may be sensitive toparticular frequencies of radio signals, and such frequencies would needto be avoided or the specimen appropriately shielded when designing thesystem 100.

The inventory and management software 104 is tailored for use withwireless communication systems and the processing of data associatedwith the life sciences. It consists of a customized user interface and aset of predefined database tables in one embodiment. A user can entersample-associated data or import information from outside sources.Predefined tables are provided in the database to facilitate setup ofthe system, but a user can have the option to customize fields withinthe tables. The relational database can include tables for DNA sample,clones, oligonucleotides, PCR fragments, cDNA, chemical compounds,proteins, metabolites, lipids, cellular fractions, biological samplesfrom different organisms such as viruses, bacteria, or multi-cellularorganisms, patient samples such as blood, urine, and buccal swabs.Detailed sample information and sample-associated data is programmedinto the tables. Sample information can for example include samplesource, clone name, gene insert name, insert size, insert sequence,modifications, vector name, vector size, antibiotic selection,induction, terminator, cloning sight, 5′-tag, 3′-tag, purification tag,oligonucleotide name, purification, quality control, forward primer,reverse primer, T_(m) value, and size selection. Clinical patientinformation can be, for example, age, gender, location, ethnic group,body mass index, family history, medication, data of onset of symptoms,duration of disease, and medical tests. Sample-associated data canconsist of research data from various sources, such as, for example,sequence information from a DNA sequencer, transcriptional profilinginformation from microarray chips, protein data from Western blotting orin-situ hybridization, bioassay data for drug discovery, highthrough-put drug screening data, chemical library synthesis data, andthe like. Data can be supplied in the form of text, numbers, tables, orimages.

The software can also link to other data sources and integrateinformation from public domains, such as GenBank, SwissProt, and othersimilar domains or proprietary sources. Ideally the software is able tointerface with robotics equipment to track the sample within a process,and tracking of the process can be displayed as an accumulative samplehistory for storage within the sample device as well as the database,such as storage in an RFID transponder 110.

The software is designed to create an informatics infrastructure where asingle user generates their data and information set, which is initiallystored at a local workstation in a local database format. However, thesoftware is capable of linking multiple users in a hierarchicalenvironment. The information accumulated by a single user can best beup-loaded to a centralized database system on a server. The interactionof the network environment can also be a web browser interface. Themulti-user environment can be expanded to multiple-site environments,and software and databases can be located on a personal computer, on aserver within an intranet or on the internet such as an e-commerce site.Access control and log control systems are also provided in thesoftware.

Shown in FIG. 11 is a computer-implemented system architecture 114 forutilizing a local area network 116 to interface an application processor118 with one or more interrogators 120 that communicate with one or moreremote RFID tags 122. The application processor 118 is coupled to adatabase 124 It is to be understood that the local area network caninstead be a global network, such as the Internet, in which caseweb-based applications would be utilized.

Ideally, in one embodiment the inventory and management software 104 hasthree components, a front end software component, a middlewarecomponent, and a back end software component.

It is envisioned that the front end software is utilized to create a“user interface.” This can be, for example, a web browser or MicrosoftExcel. The web browser software would be used for a web-based system100, whereas the Microsoft Excel software would be used for a desktopsystem. The web-based option provides for multiple users, networking,and can be expanded to accommodate thousands of users. The desktopoption is sufficient for a single user who does not anticipate sharingof data and sample information via a network.

The middleware can include Microsoft Excel macros developed for use as adesktop option or custom software created by programming languagesuitable for use with web-based systems, such as PHP. The middleware isconfigured as a collection of programs that is capable of receiving userinputs and queries and returning database information to the user viaknown output, such as printer, display, or audible output.

The back end software is preferably Microsoft Access, which isproprietary database software offered by Microsoft Corporation andhosted by Microsoft Excel. This particular program provides sufficientdatabase capacity to support up to 50,000 records, and to a maximum of100,000 records with increasing levels of performance degradation.Another option is MySQL, which is a freeware database software developedcollaboratively and available at no charge that runs on all majorservers, including those based on Windows and Linux platforms. Thisdatabase is capable of handling millions of records, and would besuitable for the large institutional user, such as governmentalagencies, universities, and multinational entities.

The software 104 is configured to provide control signals to the RFIDinterface 108 and to receive data and information from the interface108. In addition, when information is supplied to a transponder, thesoftware 104 is configured to initiate writing of the data through theinterrogator 112 to the transponder 110 using methods and equipmentknown in the art and which is readily commercially available.

FIG. 12 illustrates another system architecture 128 in which a database130 is linked to a plurality of desktop computers 132 via a web server134. Resident on the server 134 is software that provides acommunication layer between the user, the database 130, and desktopsoftware 136 resident on the desktop computers 132. With a web browserinterface 138, a user can connect to the RFID reader 142 through astandard USB connection 140. The user can then control read and writeoperations of the RFID reader 142 and the remote RFID tag 144 using thewireless connection 146 provided by the radio frequency communications.

Referring next to FIG. 13, shown therein is a further embodiment of theinvention utilizing a 3-tier architecture 148 having a desktop computer150 with a front-end web browser 158 linked to a backend database 154via web server middleware 156 on a web server 152. The middlewaresearch, retrieval, and display ability to a user. More particularly, thebusiness logic is contained in the middleware program 156 on the webserver 152. In addition, there is (optionally) an RFID reader 160coupled via a USB connection 162 to the client-side program 164 on thedesktop computer 150. The client-side application, which reads andwrites to the RFID tag 166 via the reader 160, is launched from the webbrowser 158.

In an alternative 2-tier arrangement of this architecture 148, there isan Excel front-end program on the desktop computer 150 that communicatesdirectly with the database 154 at the back end. The business logic hereis embodied in the Excel macro program. This method is particularlyefficient for loading data (e.g., 96 rows of data corresponding to eachwell in a plate) into a database to take advantage of the Excelfunctions, such as copying, dragging down, etc.

In a further alternative 2-tier arrangement of the architecture 148, astand-alone client application 170 at the front end communicatesdirectly with the database 154 at the back end. The business logic iscontained within the stand-alone client application, and a module forreading from and writing to the RFID tag 166 may also be containedwithin this application 170. Here the advantage is that the applicationis compiled (the source code is not visible) and does not requirethird-party software (Excel, web-server). The drawback is that it is notas network compatible as the 3-tier architecture described above.

The following Examples are presented by way of illustration and notlimitation.

EXAMPLES Example 1 Preparation of Matrix for Biological Sample StorageDevice

This example describes preparation of biological sample storage devicesusing a dissolvable matrix material. Dependent on the biologicalmaterial being stored in a particular example, the matrix was preparedwith different storage buffers. In these Examples, all reagents werefrom Sigma (St. Louis, Mo.) unless otherwise noted. For dry storage ofnucleic acids, 20 mM Tris pH 6.5 was used for the preparation of a 1%polyvinyl alcohol (PVA, Sigma no. P8136) basic storage matrix. Theconcentration of the polymer was tested in a range of 0.1% to 10% (v/w).The pH of the matrix was tested in the range of pH 5 to 8. Forconvenient detection of biological sample phenol red was added to theliquid matrix at 0.0002% (w/v).

The matrix in liquid form was applied to sample wells of a 96-well plateand dried completely at room temperature either under standard pressureor under vacuum in a vacuum chamber. The drying time for a 50 μl volumeof matrix was overnight and under vacuum a shorter drying time wasrequired. The plates were then ready for the storage of biologicalmaterial.

Additional storage additives such as one or more of EDTA, NaCl, MgCl₂,KCl, (NH₄)₂SO₄, MgSO₄, CaCl₂, Zn-acetate, Na-Acetate, cysteine,dithiothreitol (DTT, Cleland's reagent), potassium acetate,Tris-acetate, magnesium acetate, KPO₄, glycerol, Triton X-100®, sodiumdodecyl sulfate (SDS), sodium azide, protease inhibitors (PMSF,aminoethylbenzenesulfonyl fluoride, pepstatin, E64, bestatin, leupeptin,aprotinin), 2-mercaptoethanol, polyethylene glycol (PEG), bovine serumalbumin (BSA), nicotinic adenine dinucleotide (NAD), ATP may be addeddirectly into the storage matrix for stabilization and activation afterrehydration, depending on the bioactivity to be tested. For biologicalmaterial associated with biological activity such as enzymes, thereaction conditions may be adjusted directly in the storage matrix. Insome cases the only substance to be added for rehydration prior to anactivity reaction is water. The matrix can also include one or moreinhibitors such as antibacterial and/or antifungal agents. The matrixcan be sterilized through sterile filtration or autoclaving prior toaliquoting the matrix into the individual storage wells. The autoclavedmatrix is applied in aliquots to the storage wells either in singletubes or in multiwell plates at a liquid volume of 10 to 100 μl per wellin the case of a 96-well plate.

Example 2 Dry Storage of Nucleic Acids

Biological sample storage devices were prepared as described inExample 1. General molecular biology materials and methods were used, asdescribed. (Sambrook et al., Molecular Cloning: A Laboratory Manual,Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 2001; Ausubelet al., 1993 Current Protocols in Molecular Biology, Greene Publ. Assoc.Inc. & John Wiley & Sons, Inc., Boston, Mass.). Stability tests wereperformed for plasmids, oligonucleotides, DNA fragments in the form of a1 kB ladder, PCR products, genomic DNA (feline and human) and RNA.Recovery and stability tests were performed using gel based, PCR, andtransformation rate analyses.

A. Plasmid Storage

A total of 50 ng of circular plasmid (puc19) (New England Biolabs Inc.,Beverly, Mass.) at a concentration of 10 ng/μl in double distilled water(ddH₂O) was spotted on the dried dissolvable matrix in each well of a96-well polypropylene plate. The sample was dried and stored at roomtemperature. Control plasmid was stored in liquid form in a −20° C.freezer. For recovery, 50 μl of ddH₂O was applied to the dry samplewell. The sample was re-hydrated for 15 minutes and 10 μl aliquots wereused to transform DH5-alpha competent bacterial cells. The transformedcells were plated on LB agar plates and incubated overnight at 37° C.The cells on each plate were counted. Percent DNA recovery wascalculated based on the transformation of control DNA (10 ng of puc19stored at −20° C.).

DNA recovery was greater than 50% on a 5% PVA matrix following storagefor over 8 months. A 1% PVA matrix was tested at the 1 month time pointand resulted in recovery that was greater than or equivalent to thefreezer-stored DNA. Transfection rate for long-term storage was stablewith a recovery of 60% for 5% PVA matrix and 100% for the 1% matrix. Nodecrease in recovery was observed after 6 months of storage. 5% PVA didnot go into solution completely.

PCR analysis of the rehydrated sample demonstrated continued stabilityof the sample under the conditions described. Two PCR primers weredesigned (forward and reverse) amplifying a 480 bp stretch of the puc19plasmid. 5 ng of rehydrated sample was used for the amplificationreaction in comparison to 5 ng of control plasmid. The PCR reactionswere performed at low cycle numbers under nonsaturating conditions.After 8 months the dry stored material could be amplified withoutdetectable loss of amplification efficiency.

B. Oligonucleotide Storage

Two olgionucleotides (PCR primer forward and reverse) for theamplification of puc19 were spotted in a volume of 10 μl at a totalconcentration of 10 μM and 20 μM each on a 1% PVA dry storage matrix ineach well of a 96 well plate. The oligonucleotides were dried overnightat room temperature and the plate was stored at room temperature.Control oligonucleotides were stored in liquid form in a −20° C.freezer. For recovery, wells containing both oligonucleotides (PCRprimers) were rehydrated using PCR reagents containing 1×PCR buffer, 5ng of puc19 plasmid and dNTPs for 15 minutes. The rehydrated reactionmixture was transferred into PCR tubes and Taq polymerase was added. Thereaction was cycled for 25 cycles and electrophoretically analyzed on a1% agarose gel.

The gel analysis revealed the amplification of a PCR product of expectedsize. Compared to the control, twice the amount of primer was requiredto obtain the same amount of amplification compared to liquid storedprimer. Recovery rate from a 1% PVA matrix was lower than the liquidstored control. Recovery was improved by reducing the concentration ofPVA in the matrix.

C. DNA Fragment Storage

DNA fragments in the form of a 1 kb DNA ladder (Invitrogen) (0.5 ug)size standard were spotted onto a 1% PVA based dry storage matrix in thepresence of DNA loading buffer containing phenol red or other coloringagent and 50% glycerol. Each well was spotted with 10 ul of DNA ladderand dye, equivalent to the volume of fresh DNA ladder used for thevisualization of the ladder in one well of an electrophoresis agarosegel. The DNA fragments with the loading dye were dehydrated overnightand stored at room temperature. For recovery, cells with the 1 kB DNAladder size standard and loading buffer were rehydrated with 10 μl ofddH2O. The rehydration time was 5 and 10 minutes respectively, prior toloading of the 10 μl of 1 kB ladder onto an electrophoresis gel.

For analysis, 10 μl of control ladder stored in liquid form in thepresence of loading buffer at −20° C. was compared by fluorescenceintensity using Ethidium Bromide stain to the 5 minute and 10 minuterehydrated dry stored size standard. No difference in fluorescenceintensity of the different size DNA bands was observed. None of thebands showed DNA degradation from the dry storage at room temperature.

D. Genomic DNA Storage

a) Genomic Feline DNA

A total amount of 20 ng total genomic feline DNA in 10 μl of TE pH8buffer was spotted onto a 5% PVA based dry storage matrix per well of a96 well plate. The genomic DNA was dried overnight and stored at roomtemperature. Control DNA was stored frozen at −20° C. For recovery, thewells containing the genomic feline DNA were rehydrated using PCRreagents containing 1×PCR buffer, 2 feline specific primers at aconcentration of 10 μM and dNTPs for 15 minutes. The primers amplified a600 bp fragment of feline DNA. The rehydrated reaction mixture wastransferred into PCR tubes and Taq polymerase was added. The reactionwas cycled for 35 cycles and analyzed on a 1% agarose gel.

PCR analysis was performed one week and 3.5 months after dry storage. Atboth time points the DNA fragment of expected size could be amplifiedwithout a decrease in amplification rate compared to frozen storedgenomic DNA.

b) Genomic Human DNA

A total amount of 20 ng total genomic human DNA in 10 μl of TE pH8buffer was spotted onto a 1% PVA based dry storage matrix in each wellof a 96 well plate. The genomic DNA was dried overnight and stored atroom temperature. Control DNA was stored frozen at −20° C.

Wells containing the genomic human DNA were rehydrated during PCRreagents containing 1×PCR buffer, 2 human growth factor 13 (hFGF13)specific primers at a concentration of 10 μM and dNTPs for 15 minutes.The rehydrated reaction mixture was transferred into PCR tubes and Taqpolymerase was added. The reaction was cycled for 35 cycles and analyzedon a 1% agarose gel.

PCR analysis was performed one month after dry storage. The fragment ofthe human growth factor gene of expected size was amplified without adecrease in amplification rate compared to frozen stored genomic DNA.

Example 3 Dry Storage of Proteins

Biological sample storage devices were prepared as described inExample 1. This example shows that dry storage of proteins at ambienttemperature with complete recovery of activity offer tremendousadvantages compared to storage of proteins frozen as liquid samples.

Stability and activity tests for different sequenases, heat stablepolymerases, restriction enzymes, ligases, proteases were performed todemonstrate the protective nature of the dissolvable matrix.Stabilization of proteins and their recovery as active molecules wasachieved using the longterm dissolvable matrix described above. Thematrix was prepared in the presence of TRIS pH5-8, phenol red as a pHindicator, and 1% PVA. The matrix was solidified by dehydration and theproteins were spotted onto the dried matrix in the presence or absenceof trehalose (Fluka, cat. no. 90210) or validamycin A (Research ProductsInternational Corp., catalog no. V21020) in liquid form. The water inthe protein solution hydrated and solubilized the PVA. The proteinmixture soaked into the solubilized matrix and dried at ambienttemperature. Validamycin A was added to the biological material in aconcentration of 0.5 to 10% w/v. The mixture of biological sample in thepresence of validamycin A was applied to the dissolvable PVA samplematrix.

Example 4 Longterm Storage of Proteins Using the Dissolvable PVA Matrix

This example describes recovery of active proteins following longtermdry storage on dissolvable PVA matrices prepared as described in thepreceding examples.

A. Polymerases

1) SEQUENASE™—Sequenase™ (USB, Cleveland, Ohio) is normally stored at−20° C. and loses activity over time in the freezer through repeatedfreeze thaw, resulting in reduced reading length and quality of thesequencing reaction. Sequenase™ was applied to the dissolvable matrix in1× sequencing buffer in the presence of 5% final concentration oftrehalose or validamycin A. USB Sequenase™ Version 2.0, DNA sequencingkit (product number 70770) was used according to suppliers protocol. Theconcentration per well in a 96 well plate was equivalent to theconcentration of frozen stored Sequenase™ used for one sequencingreaction. Control Sequenase™ was stored conventionally, in a −20° C.freezer. For recovery, the complete well was hydrated with 20 μl of 1×sequencing buffer for 5-45 minutes.

For activity analysis, sequencing reactions were prepared using an S35label and the reaction was electrophoresed on an acrylamide sequencinggel. The sequences of the frozen and the dry stored sequenase werecompared by reading the sequence ladders. Both sequences had the samereading quality.

2) TAQ POLYMERASE—Taq polymerase for PCR reactions is stored at −20° C.and loses activity over time through repeated freeze thaw resulting inlower amplification efficiency. The Taq polymerase (5 U per well) wasapplied to the dissolvable matrix in 1×PCR buffer in the presence of 5%final concentration of Trehalose or Validamycin A. The concentration perwell in a 96 well plate was equivalent to the concentration of frozenstored Taq polymerase used for one PCR reaction. Control Taq polymerasewas stored conventionally in a −20° C. freezer. For recovery, thecomplete well was hydrated with 20 ul of 1×PCR buffer for 5-45 minutes.

For activity analysis, PCR reactions were prepared using standard PCRprotocols and the PCR product was electrophoresed on an agarose gel. ThePCR products of the frozen and the dry stored polymerase were comparedby visual inspection. Both PCR products were equal in intensity.

3) DEEP VENT™ HIGH FIDELITY POLYMERASE (New England Biolabs Inc,Beverly, Mass.) Deep Vent™ polymerase for PCR reactions was shipped ondry ice and stored at −20° C. If the frozen chain of transport wasinterrupted the enzyme lost its activity. The protein lost activity overtime through repeated freeze thaw, resulting in reduced enzyme activity.Fully active Deep Vent™ polymerase was applied to the dissolvable PVAmatrix in 1×PCR buffer in the presence of 5% final concentration ofValidamycin A. The concentration per well in a 96 well plate was (5 Uper well), equivalent to the concentration of frozen stored Deep Vent™Polymerase used for one PCR reaction. Control Deep Vent™ Polymerase wasstored in a −20° C. freezer. The complete well was hydrated with 20 μlof 1×PCR buffer for 5-45 minutes. PCR reactions were prepared usingstandard PCR protocols and the PCR product was electrophoresed on anagarose gel. As shown in FIG. 14, the PCR products of the frozen and thedry stored sequenase were compared by visual inspection. Both PCRproducts were equal in ethidium bromide intensity. No quantitativedifference could be detected between a re-hydration time of 5 minutesversus 60 minutes.

B. Restriction Enzymes

HindIII was spotted at 20 U and 40 U per well was applied to thedissolvable matrix in 1× digestion buffer in the presence of 5% finalconcentration of Trehalose or Validamycin A. The concentration per wellin a 96 well plate was equivalent to the concentration of frozen storedTaq polymerase used for one PCR reaction. Control HindIII was storedconventionally in a −20° C. freezer. The complete well was hydrated with20 μl of 1× restriction enzyme buffer for 5-45 minutes. 1 ug of puc19plasmid was digested with the rehydrated restriction enzyme and thedigested plasmid was electrophoresed on an agarose gel. The DNA bandingpattern of the frozen and the dry stored HindIII were compared to anondigested plasmid by visual inspection. The frozen and the dry storedenzyme showed equivalent activity.

C. BIG DYE™ CYCLE SEQUENCING—ABI Big Dye™ (Applied Biosystems Inc.,Foster City, Calif.) enzyme for cycle sequencing lost activity over timeafter repeated freeze thaw processes, resulting in reduced readinglength of the sequencing reaction and reduced quality of the read.

Fresh, appropriately stored, active Big Dye™ (ABI) was applied to thedissolvable PVA matrix in 1× reaction buffer in the presence of 5% finalconcentration of trehalose (Fluka #90210). To test if the Big Dye™enzyme can be dehydrated in the presence of plasmid and sequencingprimers without loss of activity, Big Dye™ was spotted in the presenceof M13 forward primer and puc19. The concentration per well in a 96 wellplate was equivalent to the concentration of frozen stored Sequenase™(USB) used for one sequencing reaction. Control Sequenase™ was stored inthe conventional in a −20° C. freezer. The complete well was hydratedwith 20 μl of 1× reaction buffer for 30 minutes. PCR reactions wereperformed according to the suppliers' recommendations for 35 cycles. ThePCR products of the cycle sequencing reaction were purified and analyzedusing an ABI capillary sequencing instrument according to themanufacturer's instructions. The sequences of the frozen and thedry-stored Big Dye™ as well as the dried Big Dye™ in the presence andabsence of the plasmid and sequencing primers were compared using MacVector sequence analysis programs. The sequence quality was identical,in the first 700 bases. Longer reads were obtained using the dried BigDye reagents, as shown in FIG. 15.

D. Proteases

Proteases are major drug targets. Currently, proteases are used forsmall molecule screens to develop new drugs against viral diseases suchas HIV. Protease assays are often difficult to perform because proteaseactivity is a delicate enzymatic reaction where baseline activity of thestored protease has to be adjusted prior to each assay. The kinetics ofthe reaction varies based on changes in protease activity after eachfreeze-thaw. This section demonstrates how dried proteases in thepresence of dissolvable matrix were protected from the loss of activityand could be activated after re-hydration without changes in theactivity profile, resulting in a tremendous time savings for any use ofthe enzyme, such as for a small molecule screening project.

1) HIV Protease—HIV protease was spotted at 25 nM concentration per wellof a 96 well plate pretreated with dissolvable PVA matrix in thepresence of activity buffer (0.5M MES, 250% Glycerol, 1M NaCl, pH5.25)containing trehalose or validamycin A at a final concentration of2.5-10% (w/v). As a control HIV protease was spotted in wells ofpolypropylene plates in the presence of trehalose or validamycin withoutthe presence of PVA matrix. The dried HIV protease was recovered in 1×Activity buffer in the presence of 150 mM Guanidine Hydrochloride.Complete recovery was achieved one hour post rehydration. Enzymaticreaction activity was followed in a kinetic study using a fluorogenicpeptide containing two fluorescent molecules in a FRET assay over a 20minute time course. The reaction was analyzed on a Packard Fusionmicrotiter plate fluorometer according to the manufacturer'sinstructions.

No enzyme activity could be restored using the HIV protease that hadbeen spotted with trehalose or validamycin A alone, in the absence ofthe dissolvable PVA matrix. By contrast, 100% of HIV protease activitywas recovered using enzyme that had been spotted on the PVA matrix inthe presence of trehalose and 70% of the activity was recovered fromenzyme that had been dried using dissolvable matrix alone (PVA) withoutadditional stabilizing agents.

2) FIV Protease—FIV (Feline Immunodeficiency Virus) is a lentivirusclosely related to HIV. The FIV protease was spotted onto wellspretreated with dried dissolvable matrix at a concentration of 0.5 μgper well in the presence and absence of the peptide based inhibitor,TL-3 (Lee et al., 1998 PNAS 95:939). The wells containing the matrix,the protease and the inhibitor TL-3 were completely dried and stored atroom temperature. The dried HIV protease was rehydrated for one hour in1× activity buffer in the presence of 150 mM Guanidine Hydrochloride.The enzymatic reaction activity was followed in a kinetic study using afluorogenic peptide containing two fluorescent molecules in a FRET assayover a 20 minute time course. The reaction was analyzed on a PackardFusion microtiter plate fluorometer. The FIV protease activity was fullyrestored after the rehydration process and the enzymatic activity wasblocked by TL-3 demonstrating that the protease and its inhibitor arefully active after dry storage at ambient temperature.

Trehalose and validamycin were also compared as described above but fortheir affects on FIV protease in protease assays for the protection ofenzyme activity during longterm dry matrix storage of the protease atambient temperature on the dissolvable storage matrix. Either additiveprotectively stabilized the enzyme and no difference was detectable forthe protection of the enzyme (FIG. 17).

E. LIGASES-T4 DNA ligase (New England Biolabs, Beverly, Mass. # M0202L)(400 U) per well was applied to the dissolvable PVA matrix prepared asdescribed above in 1× ligation buffer in the presence of 5% finalconcentration of validamycin A. Control ligase was stored in a −20° C.freezer. The complete well was hydrated with 20 μl of 1× ligation bufferfor 5-45 minutes. 50 ng of SalI digested, calf intestinal phosphatasedephosphorylated puc19 plasmid was ligated overnight with the rehydratedligase in parallel with frozen stored ligase. One half of the ligationreaction was transformed into DH5alpha competent bacterial cells. Thecells were plated on LB agar plates and the transformation rate wasanalyzed by colony counts. Only religated plasmids could form coloniesunder these conditions. The dry stored ligase had 5-fold higher colonycounts than the frozen stored ligase.

F. Reconstitutable HIV protease Assay—Currently HIV protease assaysrequire defrosting the protease, resuspension in an activity buffer,resuspension of the fluorogenic substrate in its buffer system, mixingof the solution and application of the mixture onto special fluorescent96-well plates for a pretest of the defrosted enzyme activity. Afterdetermination of the protease activity, the assay for the screening ofinhibitory compounds can begin and is usually conducted in 96 wellformat. The same procedure has to be repeated involving the pipettingsteps described above. This section shows how using the proteasesupplied according to the compositions and methods of the presentapplication on the dissolvable matrix in dried form, no pretest has tobe performed, since the HIV protease activity remained stable underdried conditions.

Using the dissolvable PVA matrix prepared as described above, HIVprotease and FIV protease were spotted and dried in their respectiveactivity buffer at the appropriate reaction concentration. Thefluorogenic protease substrate and the negative control well containingthe protease inhibitor were supplied in their buffer in dried form on 96well plates as well. The operator of the screen had only to add wateralone or containing a test inhibitor screening compound to rehydrate theprotease containing well, and water to the fluorescent substrate well.Accordingly, for rehydrating some FIV protease wells the TL-3 inhibitordescribed above was included. The handling time for the assay wasreduced by more than 10 fold, and representative results are shown inFIG. 18. Similar time savings can be obtained for other biochemicalassays, screens or experimental protocols.

Example 5 Longterm Storage of Cells Using the Dissolvable PVA Matrix

This example describes longterm dry storage at ambient temperature of E.coli cells on a dissolvable matrix material.

Equal numbers of Escherichia coli (DH5 alpha) bacteria were resuspendedin LB growth media and spotted in wells of a 96 well plate: a) withoutdissolvable matrix in growth medium, b) with dried dissolvable PVAmatrix and c) mixed with 5% validamycin A and spotted on drieddissolvable matrix. The plates were dried overnight and stored atambient temperature. The wells with the three different conditions werehydrated with growth media for one hour and the content of the wellswere plated onto bacterial culture LB plates. The plates were incubatedat 37° C. overnight. The E. coli recovery rate was analyzed throughcounting of the bacterial colonies, as shown in FIG. 19.

The dissolvable matrix is also prepared and used for the dried long-termstorage of cells, including other bacteria, plant, animal or humancells, and for dry storage of phages, viruses (e.g., lentivirus,baculovirus, etc.).

Embodiments of the dry matrix storage compositions and methods of theinvention are also contemplated for use with antibodies, RNA, enzymes,and other biological samples as provided herein.

From the foregoing, it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention. Accordingly, the invention is notlimited except as by the appended claims.

What is claimed is:
 1. A system for the storage, organization, tracking,retrieval, and analysis of nucleic acid sample, the system comprising:(i) a biological sample device comprising one or a plurality of wells,each well having disposed therein a matrix for dry storage of thenucleic acid sample without refrigeration and without lyophilization;wherein the matrix comprises at least one stabilizer, wherein if the atleast one stabilizer comprises a first stabilizer that is trehalose,then a trehalase inhibitor is also present as a second stabilizer; andwherein the matrix is free of fibers and cellulosic materials and atleast 50% of the nucleic acid sample is recovered when an aqueoussolvent is added to a the matrix; (ii) a computer-implemented system forreceiving and transmitting data regarding the sample device; and (iii) aradio frequency interface between the sample device and thecomputer-implemented system for providing a communication link betweenthe computer-implemented system and the sample device.
 2. The system ofclaim 1 wherein the radio frequency interface comprises a radiofrequency interrogator coupled to the computer-implemented system and atleast one transponder device associated with the sample storage devicefor radio frequency communication with the interrogator.
 3. The systemof claim 1 wherein the biological sample storage device furthercomprises a magnetic closure and an airtight junction around each atleast one well.